diff --git a/gamgee/variant_builder.cpp b/gamgee/variant_builder.cpp
index f4bbc0578..27122974a 100644
--- a/gamgee/variant_builder.cpp
+++ b/gamgee/variant_builder.cpp
@@ -471,7 +471,7 @@ VariantBuilder& VariantBuilder::bulk_set_individual_field(const FIELD_ID_TYPE& f
   const auto field_idx = field_index(field_id);
   if ( m_enable_validation ) {
     validate_individual_field(field_idx, provided_type);
-    validate_multi_sample_indiv_vector_length(field_values.size());
+    validate_multi_sample_vector_length(field_values);
   }
   // Need to use std::forward() here so that we can handle both the move and the copy use cases
   fields_of_type[m_indiv_field_lookup_table[field_idx]].set_entire_field(std::forward<BULK_FIELD_VALUES_TYPE>(field_values));
@@ -569,12 +569,21 @@ void VariantBuilder::validate_individual_field_existence(const int32_t field_ind
   }
 }
 
-inline void VariantBuilder::validate_multi_sample_indiv_vector_length(const uint32_t length) const {
-  if ( length == 0 || length % uint32_t(bcf_hdr_nsamples(m_header.get())) != 0 ) {
-    throw invalid_argument(string{"Number of elements in vector for individual field ("} + to_string(length) + ") not divisible by number of samples (" + to_string(uint32_t(bcf_hdr_nsamples(m_header.get()))) + ")");
+template<class ELEMENT_TYPE>
+inline void VariantBuilder::validate_multi_sample_vector_length(const std::vector<std::vector<ELEMENT_TYPE>>& vec) const {
+  const auto num_samples = uint32_t(bcf_hdr_nsamples(m_header.get()));
+  if ( vec.size() != num_samples ) {
+    throw invalid_argument(string{"Number of elements in vector of vectors for individual field ("} + to_string(vec.size()) + ") not equal to the number of samples (" + to_string(num_samples) + ")");
   }
 }
 
+template<class ELEMENT_TYPE>
+inline void VariantBuilder::validate_multi_sample_vector_length(const std::vector<ELEMENT_TYPE>& vec) const {
+  const auto num_samples = uint32_t(bcf_hdr_nsamples(m_header.get()));
+  if ( vec.size() < num_samples || vec.size() % num_samples != 0 ) {
+    throw invalid_argument(string{"Number of elements in flattened vector for individual field ("} + to_string(vec.size()) + ") not divisible by number of samples (" + to_string(num_samples) + ")");
+  }
+}
 
 void VariantBuilder::pre_build_validation() const {
   if ( (m_starting_variant_body == nullptr && (m_ref_allele.missing() || m_ref_allele.encoded_length() == 0)) ||
diff --git a/gamgee/variant_builder.h b/gamgee/variant_builder.h
index 2af0db46b..86c7dffc3 100644
--- a/gamgee/variant_builder.h
+++ b/gamgee/variant_builder.h
@@ -188,7 +188,8 @@ class VariantBuilder {
   void validate_individual_field(const int32_t field_index, const uint32_t provided_type) const;
   void validate_individual_field(const int32_t field_index, const int32_t sample_index, const uint32_t provided_type) const;
   inline void validate_individual_field_existence(const int32_t field_index) const;
-  inline void validate_multi_sample_indiv_vector_length(const uint32_t length) const;
+  template<class ELEMENT_TYPE> inline void validate_multi_sample_vector_length(const std::vector<std::vector<ELEMENT_TYPE>>& vec) const;
+  template<class ELEMENT_TYPE> inline void validate_multi_sample_vector_length(const std::vector<ELEMENT_TYPE>& vec) const;
   void pre_build_validation() const;
   void post_build_validation(const std::shared_ptr<bcf1_t>& new_variant_body) const;