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Bladder exstrophy (BE) and cloacal exstrophy (CE) are rare birth defects that have been reported to occur in 1:30,000–50,000 and 1:200,000–400,000 live births. Disagreement exists as to whether they comprise two distinct disorders or are part of a spectrum. We examined epidemiologic trends and risk factors for BE and CE in a large population‐based dataset.Potential cases were identified in the New York State (NYS) Congenital Malformations Registry. When nonspecific codes for CE were reported, narrative descriptions were reviewed for classification. Birth certificate data were analyzed with descriptive statistics and Poisson regression was used to calculate crude (PR) and adjusted prevalence ratios (aPR) and 95% confidence intervals (CI).In NYS from 1983 through 1999, 95 BE cases and 29 CE cases were identified for a live‐birth prevalence of 2.1 and 0.6 per 100,000 live births. BE showed a statistically significant downward linear trend by year. Factors associated with BE included summer conception (vs. winter, aPR 2.46, CI 1.19–5.10), white, non‐Hispanic maternal race/ethnicity (vs. black non‐Hispanic, aPR 3.20, CI 1.20–8.52), and male sex (female vs. male, aPR 0.53, CI 0.33–0.87). Factors associated with CE included preterm low birth weight birth (aPR 14.55, CI 5.28–40.07), multiple birth (aPR 6.68, CI 1.19–23.27), non‐New York City residence (aPR 3.27, CI 1.04–10.22), and female sex (aPR 2.57, CI 1.00–6.64). Infant mortality was greater in the CE group.The epidemiology suggests different risk factor patterns for BE and CE. Classification of BE and CE is difficult due to the nonspecific coding. Birth Defects Research (Part A) 79:781–787, 2007. © 2007 Wiley‐Liss, Inc.