Bardet-Biedl syndrome (BBS) and McKusick-Kaufman syndrome (MKKS) are rare congenital disorders of autosomal recessive inheritance. Because of the phenotypic overlap of both syndromes, including hydrometrocolpos (HMC) and postaxial polydactyly (PAP) in the neonatal stage, the potential for diagnostic confusion exists. A case of BBS with the initial presentation of MKKS is reported. MKKS was diagnosed during the neonatal period based on the classical findings of HMC together with vaginal atresia and PAP. However, follow-up examination after the age of 2 years revealed additional clinical features consistent with BBS, including mental retardation, obesity, and retinitis pigmentosa. A rehabilitation program was undertaken for the problems of moderate motor delay and slurred speech. MKKS may be considered as a variant of BBS. Careful monitoring for the complications of BBS including ophthalmologic, neurologic, and urologic assessments should be performed in patients with MKKS.