Reproductive and urinary tract abnormalities are a cause of infertility, reproductive inefficiency, and economic losses in goats. The aim of this study was to investigate the occurrence and nature of reproductive and urinary tract abnormalities encountered in female goats slaughtered at Nyagatare abattoir in the Eastern Province of Rwanda. Reproductive and urinary organs from 369 female goat carcasses were opened by incision and then given a thorough macroscopic examination by visually inspecting and palpating for evidence of abnormalities. The results showed that there was an overall occurrence of 7.8% reproductive organ/tract abnormalities and 10.6% urinary organ/tract abnormalities. Ovarian hypoplasia was the reproductive abnormality with the highest overall occurrence (32.3%) and renal calculi were the urinary organ abnormality with the highest occurrence (38.1%). 95.2% of the reproductive organ/tract abnormalities observed usually result in infertility and 91.3% of the urinary organ/tract abnormalities observed result in economic losses through condemnation of kidneys at slaughter. The high incidence of the observed urinary organ/tract abnormalities represents a potential public health challenge. There was no significant difference in the occurrence of reproductive organ/tract abnormalities according to breed (p > 0.05, n = 31). There was also no significant difference in the occurrence of urinary organ abnormalities according to breed (p > 0.05, n = 42).