diff --git a/c/CHANGELOG.rst b/c/CHANGELOG.rst
index fdbbffd160..b30c95b003 100644
--- a/c/CHANGELOG.rst
+++ b/c/CHANGELOG.rst
@@ -7,6 +7,10 @@
 - Change the type of genotypes to ``int32_t``, removing the TSK_16_BIT_GENOTYPES flag option.
   (:user:`benjeffery`, :issue:`463`, :pr:`2108`)
 
+- ``tsk_variant_t`` now includes its ``tsk_site_t`` rather than pointing to it. 
+  (:user:`benjeffery`, :issue:`2161`, :pr:`2162`)
+
+
 **Features**
 
 - Make dumping of tables and tree sequences to disk a zero-copy operation.
diff --git a/c/tests/test_genotypes.c b/c/tests/test_genotypes.c
index 465fa13652..ddbafac8ff 100644
--- a/c/tests/test_genotypes.c
+++ b/c/tests/test_genotypes.c
@@ -47,7 +47,7 @@ test_simplest_missing_data(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_TRUE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], TSK_MISSING_DATA);
     CU_ASSERT_EQUAL(var->genotypes[1], TSK_MISSING_DATA);
@@ -59,7 +59,7 @@ test_simplest_missing_data(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_FALSE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], 0);
     CU_ASSERT_EQUAL(var->genotypes[1], 0);
@@ -91,7 +91,7 @@ test_simplest_missing_data_user_alleles(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_TRUE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], TSK_MISSING_DATA);
     CU_ASSERT_EQUAL(var->genotypes[1], TSK_MISSING_DATA);
@@ -103,7 +103,7 @@ test_simplest_missing_data_user_alleles(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_TRUE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], TSK_MISSING_DATA);
     ret = tsk_vargen_next(&vargen, &var);
@@ -114,7 +114,7 @@ test_simplest_missing_data_user_alleles(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_FALSE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], 0);
     CU_ASSERT_EQUAL(var->genotypes[1], 0);
@@ -148,7 +148,7 @@ test_simplest_missing_data_mutations(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_TRUE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], 1);
     CU_ASSERT_EQUAL(var->genotypes[1], TSK_MISSING_DATA);
@@ -161,7 +161,7 @@ test_simplest_missing_data_mutations(void)
     tsk_vargen_print_state(&vargen, _devnull);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_FALSE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], 1);
     ret = tsk_vargen_next(&vargen, &var);
@@ -172,7 +172,7 @@ test_simplest_missing_data_mutations(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_FALSE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], 1);
     CU_ASSERT_EQUAL(var->genotypes[1], 0);
@@ -207,7 +207,7 @@ test_simplest_missing_data_mutations_all_samples(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_FALSE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], 1);
     CU_ASSERT_EQUAL(var->genotypes[1], 1);
@@ -220,7 +220,7 @@ test_simplest_missing_data_mutations_all_samples(void)
     tsk_vargen_print_state(&vargen, _devnull);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_FALSE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], 1);
     CU_ASSERT_EQUAL(var->genotypes[1], 1);
@@ -232,7 +232,7 @@ test_simplest_missing_data_mutations_all_samples(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_FALSE(var->has_missing_data);
     CU_ASSERT_EQUAL(var->genotypes[0], 1);
     CU_ASSERT_EQUAL(var->genotypes[1], 1);
@@ -273,7 +273,7 @@ test_single_tree_user_alleles(void)
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_EQUAL_FATAL(var->num_alleles, 4);
     CU_ASSERT_EQUAL(var->allele_lengths[0], 1);
     CU_ASSERT_EQUAL(var->allele_lengths[1], 1);
@@ -291,7 +291,7 @@ test_single_tree_user_alleles(void)
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.125);
+    CU_ASSERT_EQUAL(var->site.position, 0.125);
     CU_ASSERT_EQUAL(var->num_alleles, 4);
     CU_ASSERT_EQUAL(var->allele_lengths[0], 1);
     CU_ASSERT_EQUAL(var->allele_lengths[1], 1);
@@ -309,7 +309,7 @@ test_single_tree_user_alleles(void)
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.25);
+    CU_ASSERT_EQUAL(var->site.position, 0.25);
     CU_ASSERT_EQUAL(var->num_alleles, 4);
     CU_ASSERT_EQUAL(var->allele_lengths[0], 1);
     CU_ASSERT_EQUAL(var->allele_lengths[1], 1);
@@ -327,7 +327,7 @@ test_single_tree_user_alleles(void)
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.5);
+    CU_ASSERT_EQUAL(var->site.position, 0.5);
     CU_ASSERT_EQUAL(var->num_alleles, 4);
     CU_ASSERT_EQUAL(var->allele_lengths[0], 1);
     CU_ASSERT_EQUAL(var->allele_lengths[1], 1);
@@ -377,7 +377,7 @@ test_single_tree_char_alphabet(void)
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.0);
+    CU_ASSERT_EQUAL(var->site.position, 0.0);
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_EQUAL(var->allele_lengths[0], 1);
     CU_ASSERT_EQUAL(var->allele_lengths[1], 1);
@@ -391,7 +391,7 @@ test_single_tree_char_alphabet(void)
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.125);
+    CU_ASSERT_EQUAL(var->site.position, 0.125);
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_EQUAL(var->allele_lengths[0], 1);
     CU_ASSERT_EQUAL(var->allele_lengths[1], 8);
@@ -405,7 +405,7 @@ test_single_tree_char_alphabet(void)
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.25);
+    CU_ASSERT_EQUAL(var->site.position, 0.25);
     CU_ASSERT_EQUAL(var->num_alleles, 4);
     CU_ASSERT_EQUAL(var->allele_lengths[0], 1);
     CU_ASSERT_EQUAL(var->allele_lengths[1], 1);
@@ -423,7 +423,7 @@ test_single_tree_char_alphabet(void)
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
-    CU_ASSERT_EQUAL(var->site->position, 0.5);
+    CU_ASSERT_EQUAL(var->site.position, 0.5);
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_EQUAL(var->allele_lengths[0], 1);
     CU_ASSERT_EQUAL(var->allele_lengths[1], 1);
@@ -465,8 +465,8 @@ test_single_tree_binary_alphabet(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 0);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 1);
+    CU_ASSERT_EQUAL(var->site.id, 0);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 1);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -477,8 +477,8 @@ test_single_tree_binary_alphabet(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 1);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 2);
+    CU_ASSERT_EQUAL(var->site.id, 1);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 2);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -489,8 +489,8 @@ test_single_tree_binary_alphabet(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 2);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 4);
+    CU_ASSERT_EQUAL(var->site.id, 2);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 4);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -528,8 +528,8 @@ test_single_tree_non_samples(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 0);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 1);
+    CU_ASSERT_EQUAL(var->site.id, 0);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 1);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -538,8 +538,8 @@ test_single_tree_non_samples(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 1);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 2);
+    CU_ASSERT_EQUAL(var->site.id, 1);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 2);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -548,8 +548,8 @@ test_single_tree_non_samples(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 2);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 4);
+    CU_ASSERT_EQUAL(var->site.id, 2);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 4);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -661,8 +661,8 @@ test_single_tree_subsample(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 0);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 1);
+    CU_ASSERT_EQUAL(var->site.id, 0);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 1);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -671,8 +671,8 @@ test_single_tree_subsample(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 1);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 2);
+    CU_ASSERT_EQUAL(var->site.id, 1);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 2);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -681,8 +681,8 @@ test_single_tree_subsample(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 2);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 4);
+    CU_ASSERT_EQUAL(var->site.id, 2);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 4);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -700,24 +700,24 @@ test_single_tree_subsample(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 0);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 1);
+    CU_ASSERT_EQUAL(var->site.id, 0);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 1);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 1);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 2);
+    CU_ASSERT_EQUAL(var->site.id, 1);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 2);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 2);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 4);
+    CU_ASSERT_EQUAL(var->site.id, 2);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 4);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -827,8 +827,8 @@ test_single_tree_silent_mutations(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 0);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 2);
+    CU_ASSERT_EQUAL(var->site.id, 0);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 2);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -839,8 +839,8 @@ test_single_tree_silent_mutations(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 1);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 3);
+    CU_ASSERT_EQUAL(var->site.id, 1);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 3);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -851,8 +851,8 @@ test_single_tree_silent_mutations(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 2);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 4);
+    CU_ASSERT_EQUAL(var->site.id, 2);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 4);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
@@ -863,8 +863,8 @@ test_single_tree_silent_mutations(void)
     CU_ASSERT_EQUAL(var->num_alleles, 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->site->id, 3);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 1);
+    CU_ASSERT_EQUAL(var->site.id, 3);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 1);
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
@@ -874,7 +874,7 @@ test_single_tree_silent_mutations(void)
 }
 
 static void
-test_multiple_tree_get_variant(void)
+test_multiple_variant_decode(void)
 {
     int ret = 0;
     tsk_size_t k;
@@ -933,7 +933,7 @@ test_multiple_tree_get_variant(void)
 }
 
 static void
-test_tree_get_variant_errors(void)
+test_variant_decode_errors(void)
 {
     int ret = 0;
     tsk_treeseq_t ts;
@@ -948,6 +948,13 @@ test_tree_get_variant_errors(void)
     CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_OUT_OF_BOUNDS);
     tsk_variant_free(&var);
 
+    /* Site out of bounds */
+    ret = tsk_variant_init(&var, &ts, NULL, 0, NULL, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+    ret = tsk_variant_decode(&var, 42, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_SITE_OUT_OF_BOUNDS);
+    tsk_variant_free(&var);
+
     tsk_treeseq_free(&ts);
 }
 
@@ -970,8 +977,8 @@ main(int argc, char **argv)
         { "test_single_tree_subsample", test_single_tree_subsample },
         { "test_single_tree_many_alleles", test_single_tree_many_alleles },
         { "test_single_tree_silent_mutations", test_single_tree_silent_mutations },
-        { "test_multiple_tree_get_variant", test_multiple_tree_get_variant },
-        { "test_tree_get_variant_errors", test_tree_get_variant_errors },
+        { "test_multiple_variant_decode", test_multiple_variant_decode },
+        { "test_variant_decode_errors", test_variant_decode_errors },
         { NULL, NULL },
     };
 
diff --git a/c/tests/test_trees.c b/c/tests/test_trees.c
index 411dc856e3..35f165cdee 100644
--- a/c/tests/test_trees.c
+++ b/c/tests/test_trees.c
@@ -506,9 +506,9 @@ verify_simplify_genotypes(tsk_treeseq_t *ts, tsk_treeseq_t *subset,
         CU_ASSERT_EQUAL_FATAL(ret, 1);
         ret = tsk_vargen_next(&subset_vargen, &subset_variant);
         CU_ASSERT_EQUAL_FATAL(ret, 1);
-        CU_ASSERT_EQUAL(variant->site->id, (tsk_id_t) j)
-        CU_ASSERT_EQUAL(subset_variant->site->id, (tsk_id_t) j)
-        CU_ASSERT_EQUAL(variant->site->position, subset_variant->site->position);
+        CU_ASSERT_EQUAL(variant->site.id, (tsk_id_t) j)
+        CU_ASSERT_EQUAL(subset_variant->site.id, (tsk_id_t) j)
+        CU_ASSERT_EQUAL(variant->site.position, subset_variant->site.position);
         for (k = 0; k < num_samples; k++) {
             CU_ASSERT_FATAL(sample_index_map[samples[k]] < (tsk_id_t) ts->num_samples);
             a1 = variant->genotypes[sample_index_map[samples[k]]];
@@ -1662,8 +1662,8 @@ test_simplest_back_mutations(void)
     CU_ASSERT_EQUAL(var->genotypes[0], 0);
     CU_ASSERT_EQUAL(var->genotypes[1], 1);
     CU_ASSERT_EQUAL(var->genotypes[2], 0);
-    CU_ASSERT_EQUAL(var->site->id, 0);
-    CU_ASSERT_EQUAL(var->site->mutations_length, 2);
+    CU_ASSERT_EQUAL(var->site.id, 0);
+    CU_ASSERT_EQUAL(var->site.mutations_length, 2);
     tsk_vargen_free(&vargen);
 
     tsk_treeseq_free(&ts);
diff --git a/c/tskit/genotypes.c b/c/tskit/genotypes.c
index 24a8478435..8fbc537bd5 100644
--- a/c/tskit/genotypes.c
+++ b/c/tskit/genotypes.c
@@ -141,11 +141,7 @@ tsk_variant_init(tsk_variant_t *self, const tsk_treeseq_t *tree_sequence,
     tsk_size_t num_samples_alloc;
 
     tsk_memset(self, 0, sizeof(tsk_variant_t));
-    self->site = malloc(sizeof(*self->site));
-    if (self->site == NULL) {
-        ret = TSK_ERR_BAD_PARAM_VALUE;
-        goto out;
-    }
+
     self->tree_sequence = tree_sequence;
     ret = tsk_tree_init(
         &self->tree, tree_sequence, samples == NULL ? TSK_SAMPLE_LISTS : 0);
@@ -274,7 +270,6 @@ tsk_variant_free(tsk_variant_t *self)
     tsk_safe_free(self->alt_samples);
     tsk_safe_free(self->alt_sample_index_map);
     tsk_safe_free(self->traversal_stack);
-    tsk_safe_free(self->site);
     return 0;
 }
 
@@ -470,12 +465,12 @@ tsk_variant_decode(
     int (*update_genotypes)(tsk_variant_t *, tsk_id_t, tsk_id_t);
     tsk_size_t (*mark_missing)(tsk_variant_t *);
 
-    ret = tsk_treeseq_get_site(self->tree_sequence, site_id, self->site);
+    ret = tsk_treeseq_get_site(self->tree_sequence, site_id, &self->site);
     if (ret != 0) {
         goto out;
     }
 
-    ret = tsk_tree_seek(&self->tree, self->site->position, 0);
+    ret = tsk_tree_seek(&self->tree, self->site.position, 0);
     if (ret != 0) {
         goto out;
     }
@@ -502,15 +497,15 @@ tsk_variant_decode(
 
     if (self->user_alleles) {
         allele_index = tsk_variant_get_allele_index(
-            self, self->site->ancestral_state, self->site->ancestral_state_length);
+            self, self->site.ancestral_state, self->site.ancestral_state_length);
         if (allele_index == -1) {
             ret = TSK_ERR_ALLELE_NOT_FOUND;
             goto out;
         }
     } else {
         /* Ancestral state is always allele 0 */
-        self->alleles[0] = self->site->ancestral_state;
-        self->allele_lengths[0] = self->site->ancestral_state_length;
+        self->alleles[0] = self->site.ancestral_state;
+        self->allele_lengths[0] = self->site.ancestral_state_length;
         self->num_alleles = 1;
         allele_index = 0;
     }
@@ -534,8 +529,8 @@ tsk_variant_decode(
     if (!impute_missing) {
         num_missing = mark_missing(self);
     }
-    for (j = 0; j < self->site->mutations_length; j++) {
-        mutation = self->site->mutations[j];
+    for (j = 0; j < self->site.mutations_length; j++) {
+        mutation = self->site.mutations[j];
         /* Compute the allele index for this derived state value. */
         allele_index = tsk_variant_get_allele_index(
             self, mutation.derived_state, mutation.derived_state_length);
diff --git a/c/tskit/genotypes.h b/c/tskit/genotypes.h
index 8f006a1fdd..d906419622 100644
--- a/c/tskit/genotypes.h
+++ b/c/tskit/genotypes.h
@@ -36,7 +36,7 @@ extern "C" {
 
 typedef struct {
     const tsk_treeseq_t *tree_sequence;
-    tsk_site_t *site;
+    tsk_site_t site;
     tsk_tree_t tree;
     const char **alleles;
     tsk_size_t *allele_lengths;
diff --git a/python/_tskitmodule.c b/python/_tskitmodule.c
index 32afc2da8a..3483e2491d 100644
--- a/python/_tskitmodule.c
+++ b/python/_tskitmodule.c
@@ -592,7 +592,7 @@ make_variant(tsk_variant_t *variant, tsk_size_t num_samples)
         goto out;
     }
     memcpy(PyArray_DATA(genotypes), variant->genotypes, num_samples * sizeof(int32_t));
-    ret = Py_BuildValue("iOO", variant->site->id, genotypes, alleles);
+    ret = Py_BuildValue("iOO", variant->site.id, genotypes, alleles);
 out:
     Py_XDECREF(genotypes);
     Py_XDECREF(alleles);