BACKGROUND: Little is known about the main epidemiologic characteristics of hypospadias prevalence in China. We investigated the time trends and geographic variations in the prevalence of hypospadias in China from 1996 to 2008. METHODS: Data were retrieved from the hospital-based birth defects monitoring system in China from 1996 to 2008. We used prevalence ratios (PRs) to describe the difference in prevalence of hypospadias between urban and rural areas, as well as among different regions. Poisson regression was used to explore the long time trend for the prevalence of hypospadias and its regional disparity. RESULTS: The prevalences of hypospadias for isolated anomalies, multiple anomalies, and overall cases were 7.64, 1.39, and 9.03 per 10,000 births, respectively. The national PRs (urban vs. rural) of hypospadias for overall and isolated cases were 1.25 (95% confidence interval [CI], 1.16–1.35) and 1.27 (95% CI, 1.17–1.38), respectively. The highest prevalence (12.10 per 10,000 births) was observed in the eastern region. A positive correlation was found between the prevalence of hypospadias and maternal age (p < 0.01). The average annual increase of 7.43% (95% CI, 5.52–9.38%) was observed in the overall prevalence of hypospadias in China; it was 5.28% (95% CI, 4.16–6.43%) in urban areas, 9.79% (95% CI, 7.72–11.90%) in rural areas, 9.08% (95% CI, 6.36–11.86%) in the eastern region, 4.76% (95% CI, 2.93–6.62%) in the central region, and 6.57% (95% CI, 4.44–8.74%) in the western region.CONCLUSION: The increasing trends and differences of hypospadias prevalence by urban-rural classification and geographical location suggest that environmental exposure and maternal age might have a critical role in the development of hypospadias. Birth Defects Research (Part A), 2012. © 2011 Wiley Periodicals, Inc.