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Background: Comprehensive reports on male baboon urogenital pathology are not available., Methods: We performed a retrospective study of 2246 male baboon necropsy records over 19 years., Results: A total of 289 urogenital lesions were diagnosed in 197 (8.8%) baboons. The most frequently affected organs in decreasing order were kidney, testicle, urinary bladder, penis and prepuce, seminal vesicle, ureter, and prostate. Lesions were rare in the urethra, scrotum, and epididymis. The most common diagnoses in decreasing order were nephritis, urinary bladder cystitis, nephrocalcinosis, pyelonephritis, renal cysts, renal amyloidosis, testicular atrophy, penile/preputial dermatitis, hydronephrosis, orchitis/testicular abscess, glomerulonephritis, renal hemorrhage, hypospadia, nephrosis, renal infarct, hypospermia/aspermia, seminal vesicle mineralization, and hydroureter. We also report six cases of hypospadia, the first report in the baboon., Conclusions: The male baboon has a low incidence of urogenital disease and renal disease is the most common malady. The role of herpesvirus papio 2 needs further study.