This study reports on the toxic effects of 35-days intragastric perfusion of pharmaceutical wastewater on the male reproductive system of Mus musculus. Flow cytometric analyses and staining with fluorescein diacetate (FDA) and propidium iodide (PI) were used to assess the toxicity on spermatogenic cells. Significant depletions in the relative percentages of elongated spermatid (HC), diploid spermatogonia (2C), and S-phase cells were observed. These alterations in different germ cell populations were reflected in the various germ cell ratios. The ratios of 1C:4C and HC:2C showed a significant decline after pharmaceutical wastewater treatment, while the 4C:2C and 1C:2C ratios increased significantly. FDA and PI staining displayed reduced viability of spermatogenic cells in wastewater treated group. Statistically significant percentages of sperm abnormalities showed the genotoxic potential of this pharmaceutical wastewater. Testicular histopathological studies of treated animals revealed expansion of interstitial space and reduction in the number and size of Leydig cells. Thus, the present study has established the toxicity of pharmaceutical wastewater on the reproductive biology of male mice.