Anecdotal evidence suggests that complex congenital genitourinary anomalies are occurring less frequently. However, few epidemiological studies are available to confirm or refute this suggestion. The Kids' Inpatient Database (KID) is a national, all payer database of several million inpatient pediatric hospitalizations per year, including complicated and uncomplicated in-hospital births. We reviewed the 1997 to 2009 KID to determine the birth prevalence of spina bifida, posterior urethral valves, bladder exstrophy, epispadias, prune belly syndrome, ambiguous genitalia and imperforate anus. For posterior urethral valves and prune belly syndrome we limited our search to newborn males only. During the study period, there was a diagnosis of spina bifida in 3,413 neonates, bladder exstrophy in 214, epispadias in 1,127, ambiguous genitalia in 726, prune belly syndrome in 180, posterior urethral valves in 578 and imperforate anus in 4,040. We identified no significant change in the birth prevalence of spina bifida (from 33.9 new spina bifida births of 100,000 uncomplicated births to 29.0/100,000, p = 0.08), posterior urethral valves (from 10.4/100,000 to 11.0/100,000, p = 0.51), prune belly syndrome (from 4.8/100,000 to 3.3/100,000, p = 0.44) or ambiguous genitalia (from 5.82/100,000 to 5.87/100,000, p = 0.38). There was a significant decrease in the birth prevalence of bladder exstrophy (from 2.4/100,000 to 1.6/100,000 uncomplicated births, p = 0.01) and a significant increase in epispadias (from 8.0/100,000 to 11.6/100,000) and imperforate anus (from 33.6/100,000 to 35.0/100,000, each p = 0.04) during the study period. The birth prevalence of spina bifida, posterior urethral valves and prune belly syndrome appears to have been stable in the last 12 years. Epispadias, ambiguous genitalia and imperforate anus diagnoses in newborns became more common in the same period, while bladder exstrophy diagnoses became less common.