diff --git a/tests/cases/dummy_phased_blank.vcf.gz b/tests/cases/dummy_phased_blank.vcf.gz
new file mode 100644
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diff --git a/tests/cases/dummy_phased_blank.vcf.gz.tbi b/tests/cases/dummy_phased_blank.vcf.gz.tbi
new file mode 100644
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diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py
index dbb3cb5dc6516d5a5025b44b6e5b11aefeac1f23..ec177393b8ed0ff7c2aa8eb6648276c9cc929a53 100644
--- a/tests/test_evaluate.py
+++ b/tests/test_evaluate.py
@@ -133,3 +133,27 @@ def test_truncated_positive_no_call(NA12878_positive_truncated):
     """ Variants which are missing from the positive vcf do not count towards
     alleles_no_call """
     assert NA12878_positive_truncated['alleles_no_call'] == 0
+
+
+def test_phased_positive():
+    """ Test error message when the positive vcf contains phased variants """
+    filename = 'tests/cases/gatk.vcf.gz'
+    phased = 'tests/cases/dummy_phased_blank.vcf.gz'
+    call = VCF(filename, gts012=True)
+    phased = VCF(phased, gts012=True)
+    with pytest.raises(NotImplementedError,
+                       match='Phased variants are not supported'):
+        site_concordancy(call, phased, call_samples=['NA12878'],
+                         positive_samples=['BLANK'])
+
+
+def test_phased_call():
+    """ Test error message when the call vcf contains phased variants """
+    filename = 'tests/cases/gatk.vcf.gz'
+    phased = 'tests/cases/dummy_phased_blank.vcf.gz'
+    call = VCF(phased, gts012=True)
+    positive = VCF(filename, gts012=True)
+    with pytest.raises(NotImplementedError,
+                       match='Phased variants are not supported'):
+        site_concordancy(call, positive, call_samples=['BLANK'],
+                         positive_samples=['NA12878'])
diff --git a/vtools/evaluate.py b/vtools/evaluate.py
index 652dd3396099ee30b378ca6a592770389d866d5f..ea276ca08a3a54b533b4b46e56290e8b5b53b145 100644
--- a/vtools/evaluate.py
+++ b/vtools/evaluate.py
@@ -165,6 +165,10 @@ def site_concordancy(call_vcf: VCF,
             pos = pos_record.genotypes[p_s]
             cal = call_record.genotypes[c_s]
 
+            # If the genotypes are phased
+            if pos[2] or cal[2]:
+                raise NotImplementedError('Phased variants are not supported')
+
             # Parse the genotypes and add the results into d
             parse_variants(pos, cal, d)