Neonatal hydrometrocolpos (HMC) is a rare Mullerian duct anomaly with an incidence of 0.006%. It occurs due to blockage of the vagina with accumulation of mucus secretions proximal to the obstacle. These secretions are secondary to intrauterine and postnatal stimulation of uterine and cervical glands by maternal estrogens. A triad of congenital HMC, polydactyly, and cardiac anomalies are the cardinal features of McKusick-Kaufman syndrome, which is also known as hydrometrocolpos-polydactyly syndrome. Bardet-Biedl syndrome is a well-known combination of hypogonadism, obesity, postaxial polydactyly, renal dysplasia, retinal degeneration, and mental impairment. In this case report, we describe a neonate with HMC, polydactyly, and hydronephrosis.