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Abstract Background In 2010, the World Health Assembly passed a resolution calling upon countries to prevent birth defects where possible. Though birth defects surveillance programs are an important source of information to guide implementation and evaluation of preventive interventions, many countries that shoulder the largest burden of birth defects do not have surveillance programs. This paper shares the results of a hospital-based birth defects surveillance program in Uganda which, can be adopted by similar resource-limited countries. Methods All informative births, including live births, stillbirths and spontaneous abortions; regardless of gestational age, delivered at four selected hospitals in Kampala from August 2015 to December 2017 were examined for birth defects. Demographic data were obtained by midwives through maternal interviews and review of hospital patient notes and entered in an electronic data collection tool. Identified birth defects were confirmed through bedside examination by a physician and review of photographs and a narrative description by a birth defects expert. Informative births (live, still and spontaneous abortions) with a confirmed birth defect were included in the numerator, while the total informative births (live, still and spontaneous abortions) were included in the denominator to estimate the prevalence of birth defects per 10,000 births. Results The overall prevalence of birth defects was 66.2/10,000 births (95% CI 60.5–72.5). The most prevalent birth defects (per 10,000 births) were: Hypospadias, 23.4/10,000 (95% CI 18.9–28.9); Talipes equinovarus, 14.0/10,000 (95% CI 11.5–17.1) and Neural tube defects, 10.3/10,000 (95% CI 8.2–13.0). The least prevalent were: Microcephaly, 1.6/10,000 (95% CI 0.9–2.8); Microtia and Anotia, 1.6/10,000 (95% CI 0.9–2.8) and Imperforate anus, 2.0/10,000 (95% CI 1.2–3.4). Conclusion A hospital-based surveillance project with active case ascertainment can generate reliable epidemiologic data about birth defects prevalence and can inform prevention policies and service provision needs in low and middle-income countries.