Hydrometrocolpos (HMC) and post-axial polydactyly (PAP) are common to both McKusick-Kaufman syndrome (MKS) and Bardet-Biedl syndrome (BBS). We review reported cases of MKS and BBS presenting with HMC and PAP early in life to determine if there are clinical features that allow discrimination between the two syndromes as the primary features of retinitis pigmentosa, obesity, learning disability in BBS are age-dependent. We did not find any phenotypic features that allowed reliable differentiation between the two syndromes in the neonatal period. However, uterine, ovarian, and fallopian tube anomalies are more common in BBS patients, and it may be that these clinical features prove to be useful discriminating features. We conclude that sporadic female infants with HMC and PAP cannot be diagnosed with MKS until at least age 5 years and that monitoring for the complications of BBS should be performed in these patients. Am. J. Med. Genet. 95:208–215, 2000. Published 2000 Wiley-Liss, Inc.