diff --git a/c/CHANGELOG.rst b/c/CHANGELOG.rst
index fa7b4da575..f8020afb87 100644
--- a/c/CHANGELOG.rst
+++ b/c/CHANGELOG.rst
@@ -12,6 +12,8 @@
 - ``num_tracked_samples`` and ``num_samples`` in ``tsk_tree_t`` are now typed as ``tsk_size_t``
   (:user:`benjeffery`, :issue:`1723`, :pr:`1727`)
 
+- The previously deprecated option ``TSK_SAMPLE_COUNTS`` has been removed. (:user:`benjeffery`, :issue:`1744`, :pr:`1761`).
+
 
 **Features**
 
diff --git a/c/tests/test_core.c b/c/tests/test_core.c
index f7f0a7f49d..a5ee35cec8 100644
--- a/c/tests/test_core.c
+++ b/c/tests/test_core.c
@@ -386,21 +386,6 @@ test_debug_stream(void)
     fclose(f);
 }
 
-static void
-test_warn_stream(void)
-{
-    FILE *f = fopen(_tmp_file_name, "w");
-    CU_ASSERT_FATAL(tsk_get_warn_stream() == stderr);
-    CU_ASSERT_FATAL(tsk_get_warn_stream() == stderr);
-
-    tsk_set_warn_stream(f);
-    CU_ASSERT_FATAL(tsk_get_warn_stream() == f);
-    tsk_set_warn_stream(stderr);
-    CU_ASSERT_FATAL(tsk_get_warn_stream() == stderr);
-
-    fclose(f);
-}
-
 static int
 validate_avl_node(tsk_avl_node_int_t *node)
 {
@@ -552,7 +537,6 @@ main(int argc, char **argv)
         { "test_malloc_zero", test_malloc_zero },
         { "test_malloc_overflow", test_malloc_overflow },
         { "test_debug_stream", test_debug_stream },
-        { "test_warn_stream", test_warn_stream },
         { "test_avl_empty", test_avl_empty },
         { "test_avl_sequential", test_avl_sequential },
         { "test_avl_interleaved", test_avl_interleaved },
diff --git a/c/tests/test_trees.c b/c/tests/test_trees.c
index e9cc564b5c..fda9dc7838 100644
--- a/c/tests/test_trees.c
+++ b/c/tests/test_trees.c
@@ -6135,30 +6135,6 @@ test_zero_edges(void)
     tsk_treeseq_free(&tss);
 }
 
-static void
-test_sample_counts_deprecated(void)
-{
-    tsk_treeseq_t ts;
-    tsk_tree_t tree;
-    int ret;
-    FILE *f = fopen(_tmp_file_name, "w");
-
-    tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL, NULL,
-        NULL, NULL, NULL, 0);
-    CU_ASSERT_EQUAL(tsk_treeseq_get_num_samples(&ts), 4);
-
-    tsk_set_warn_stream(f);
-    ret = tsk_tree_init(&tree, &ts, TSK_SAMPLE_COUNTS);
-    tsk_set_warn_stream(stderr);
-    CU_ASSERT_EQUAL_FATAL(ret, 0);
-
-    CU_ASSERT_FATAL(ftell(f) > 0);
-
-    fclose(f);
-    tsk_tree_free(&tree);
-    tsk_treeseq_free(&ts);
-}
-
 static void
 test_tree_sequence_metadata(void)
 {
@@ -6363,7 +6339,6 @@ main(int argc, char **argv)
         { "test_deduplicate_sites_multichar", test_deduplicate_sites_multichar },
         { "test_empty_tree_sequence", test_empty_tree_sequence },
         { "test_zero_edges", test_zero_edges },
-        { "test_sample_counts_deprecated", test_sample_counts_deprecated },
         { "test_tree_sequence_metadata", test_tree_sequence_metadata },
 
         { NULL, NULL },
diff --git a/c/tskit/core.c b/c/tskit/core.c
index f13efb2a48..8e5549702f 100644
--- a/c/tskit/core.c
+++ b/c/tskit/core.c
@@ -814,13 +814,12 @@ tsk_memcmp(const void *s1, const void *s2, tsk_size_t size)
     return memcmp(s1, s2, (size_t) size);
 }
 
-/* We can't initialise the streams to their real default values because
+/* We can't initialise the stream to its real default value because
  * of limitations on static initialisers. To work around this, we initialise
- * them to NULL and then set the value to the required standard stream
+ * it to NULL and then set the value to the required standard stream
  * when called. */
 
 FILE *_tsk_debug_stream = NULL;
-FILE *_tsk_warn_stream = NULL;
 
 void
 tsk_set_debug_stream(FILE *f)
@@ -837,21 +836,6 @@ tsk_get_debug_stream(void)
     return _tsk_debug_stream;
 }
 
-void
-tsk_set_warn_stream(FILE *f)
-{
-    _tsk_warn_stream = f;
-}
-
-FILE *
-tsk_get_warn_stream(void)
-{
-    if (_tsk_warn_stream == NULL) {
-        _tsk_warn_stream = stderr;
-    }
-    return _tsk_warn_stream;
-}
-
 /* AVL Tree implementation. This is based directly on Knuth's implementation
  * in TAOCP. See the python/tests/test_avl_tree.py for more information,
  * and equivalent code annotated with the original algorithm listing.
diff --git a/c/tskit/core.h b/c/tskit/core.h
index d04d031e38..158ffb959c 100644
--- a/c/tskit/core.h
+++ b/c/tskit/core.h
@@ -512,8 +512,6 @@ int tsk_memcmp(const void *s1, const void *s2, tsk_size_t size);
 /* Developer debug utilities. These are **not** threadsafe */
 void tsk_set_debug_stream(FILE *f);
 FILE *tsk_get_debug_stream(void);
-void tsk_set_warn_stream(FILE *f);
-FILE *tsk_get_warn_stream(void);
 
 #ifdef __cplusplus
 }
diff --git a/c/tskit/trees.c b/c/tskit/trees.c
index 483fb8058c..5b199e1381 100644
--- a/c/tskit/trees.c
+++ b/c/tskit/trees.c
@@ -3220,12 +3220,6 @@ tsk_tree_init(tsk_tree_t *self, const tsk_treeseq_t *tree_sequence, tsk_flags_t
         ret = TSK_ERR_BAD_PARAM_VALUE;
         goto out;
     }
-    if (options & TSK_SAMPLE_COUNTS) {
-        fprintf(tsk_get_warn_stream(),
-            "TSK_SAMPLE_COUNTS is no longer supported. "
-            "Sample counts are tracked by default since 0.99.3, "
-            "Please use TSK_NO_SAMPLE_COUNTS to turn off sample counts.");
-    }
     num_nodes = tree_sequence->tables->nodes.num_rows;
     num_samples = tree_sequence->num_samples;
     self->num_nodes = num_nodes;
diff --git a/c/tskit/trees.h b/c/tskit/trees.h
index 7f95504bad..4dfd230e25 100644
--- a/c/tskit/trees.h
+++ b/c/tskit/trees.h
@@ -36,13 +36,7 @@ extern "C" {
 
 #include <tskit/tables.h>
 
-/* The TSK_SAMPLE_COUNTS was removed in version 0.99.3, where
- * the default is now to always count samples except when
- * TSK_NO_SAMPLE_COUNTS is specified. This macro can be undefined
- * at some point in the future and the option reused for something
- * else. */
 // clang-format off
-#define TSK_SAMPLE_COUNTS           (1 << 0)
 #define TSK_SAMPLE_LISTS            (1 << 1)
 #define TSK_NO_SAMPLE_COUNTS        (1 << 2)