BackgroundPolydactyly is a congenital abnormality characterized by the presence of additional fingers on one or more extremities. In Colombia, polydactyly accounted for 17% of musculoskeletal congenital abnormalities in 2021, with a prevalence of 6.03 per 10,000 live births. The purpose of this study was to determine the prevalence of polydactyly and identify associated risk factors in Bogotá and Cali, Colombia, from 2002 to 2020.MethodsA retrospective case‐control study design was employed, analyzing data from birth defect reports provided by the Program for the Prevention and Follow‐up of Congenital Defects and Orphan Diseases surveillance system. Cases included live births or stillbirths with polydactyly, while controls consisted of infants without congenital abnormality, matched in terms of birth date and hospital. Prevalence of polydactyly was calculated and risk factors were assessed through odds ratios obtained by logistic regression models, considering a 95% confidence interval.ResultsAmong the 558,255 births included in the study, 848 cases of polydactyly were identified, resulting in a prevalence rate of 15.19 per 10,000 live births. Risk factors associated with polydactyly included male newborn sex, pregestational diabetes, and a family history of malformation among first‐degree relatives.ConclusionThese findings highlight the importance a surveillance system aimed to characterize populations with congenital abnormalities, providing a better option for analyzing risk factors, help improving prevention, diagnosis, notification, and optimal treatment in patients.