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Pallister–Hall and McKusick–Kaufman syndromes are developmental disorders with well defined phenotypes, distinct loci and different patterns of inheritance. The clinical features can overlap and may cause diagnostic difficulty, particularly if complex genitourinary malformations are present. A case is presented with features of both syndromes but in which a GLI3 mutation has been identified. A literature review of similar cases is presented and it is proposed that these cases probably represent the Pallister–Hall syndrome. A detailed abdominal and perineal examination should be considered in all female patients with the Pallister–Hall syndrome, looking for associated genitourinary anomalies. Conversely, all girls with features suggestive of McKusick–Kaufman syndrome require neuroimaging to look for features of the Pallister–Hall syndrome. The correct diagnosis is important so that the patient and the family may receive appropriate management. It also allows provision for an accurate recurrence risk.