BackgroundWe aimed to analyze the prevalence and trend of birth defects (BDs) in Costa Rica, where BDs are the second leading cause of infant and under‐five mortality.MethodsA descriptive analysis of selected BDs prevalence and trends from 2000 to 2019 was performed, based on data from the Costa Rican Birth Defects Register Center, the national BDs surveillance system with coverage of 98% of live births in the country. We used Joinpoint regression to identify any calendar year where a significant change in trend occurred; the annual percent change (APC) and the average annual percent change (AAPC) were determined. Marginal means and prevalence ratios by subperiod (2000–2009 as referent and 2010–2019) were estimated using Poisson regression, and compared using Wald's chi‐square tests (alpha ≤0.05).ResultsFrom 2000 to 2019, BDs occurred in 2.3% of live births (95% CI: 2.3–2.4); 73% of which were major BDs. Males presented a significantly higher prevalence (sex ratio 1.13 males/females). The trend showed an AAPC of +3.7 (p < .05) with two joinpoints, 2005 and 2013. A significant APC (+11.3) was observed during 2005–2013, within the context of improvements in the surveillance system, such as the increase in the reporting age, and the incorporation of other data sources in addition to maternity hospitals. Most of the BDs groups presented a significant upward trend. The highest AAPC was observed for the respiratory system (+11.7), congenital heart defects (+9.5), and nervous system (+8.5).ConclusionsThe BDs present a clear upward trend in the last two decades due, among other things, to a significant improvement in the surveillance system.