BACKGROUND A comprehensive survey of the prevalence of congenital anomalies in baboons has not been previously reported. We report the congenital anomalies observed over a 26-year period in a large captive baboon colony. METHODS A computer search was performed for all baboon congenital anomalies identified at necropsy and recorded on necropsy submissions. RESULTS We identified 198 congenital anomalies in 166 baboons from 9972 necropsies (1.66% of total necropsies). The nervous, urogenital, musculoskeletal, and cardiovascular systems were most commonly affected. The most common organs affected were the brain, bone, heart, testicle, kidney, penis, aorta, and skeletal muscle. The most frequent congenital anomalies were blindness, seizures, and hydrocephalus. CONCLUSIONS The baboon has an overall frequency of congenital anomalies similar to humans and other non-human primates. Although the most frequently affected systems are similar, congenital anomalies involving the digestive system appear to be less common in the baboon.