This study evaluated the effects of a commercially recommended concentration (1 mL/L) of a fungicide tebuconazole (TBZ) on testicular and epididymal histomorphometry of Artibeus lituratus, following 7 and 30-day oral exposure. TBZ30 bats showed a reduction in the percentage of tubules and seminiferous epithelium, as well as a decrease in tubule and epithelium somatic indexes, and tubular diameter. Inversely, these animals showed increased percentage of intertubular compartment, Leydig cells and blood vessels. The volume of Leydig cells and their number per gram of testis also increased in TBZ30 bats. Alterations in epididymal morphometry were observed in all regions of the organ, with increase of ductal diameter in both exposure times. These results indicate that exposure to low concentration of TBZ resulted in testicular and epididymal morphometric changes in fruit bats, mainly at 30-day exposure, suggesting that functional alterations might be occurring in these organs and impacting reproductive capacity.