Metacarpophalangeal pattern profile (MCPP) analysis was applied to patients with Pfeiffer and Chotzen syndromes, dominantly inherited types of acrocephalosyndactyly (ACS). A characteristic MCPP was obtained for the group. However, it did not discriminate between patients with Chotzen syndrome and those with Pfeiffer syndrome. Six patients in a single family showing Pfeiffer syndrome exhibited this unique MCPP profile which was not present in non-affected family members. Furthermore, three normal-appearing relatives were identified as affected by this technique, and this diagnosis was subsequently confirmed by radiographic and genetic data. The results show that: 1) the MCPP in Pfeiffer and Chotzen syndromes is unique and can be used to make the diagnosis of an ACS syndrome in persons who show few or no clinical stigmata of disease; 2) the MCPP does not discriminate between these two ACS types.