Objective: To evaluate the protective effects of probiotic microorganisms on the reproductive and nervous systems of male rats treated with acrylamide. Methods: Thirty-two rats were randomly divided into 4 groups and received normal saline through gavage (control), acrylamide 20 mg/kg body weight, acrylamide plus probiotic microorganisms (Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus bulgaricus, Lactobacillus rhamnosus, Bifidobacterium breve, Bifidobacterium infantis, Streptococcus thermophilus and fructooligosaccharides, all mixed in sachets) 20 or 200 mg/kg body weight, respectively. After 30 days, the testis, prostate, seminal vesicle and cerebellum were removed, fixed and stained with hematoxylin-eosin (H & E). The Johnsen score was used to classify spermatogenesis. Cavalieri's principle method was used to evaluate the total volume (in mm3) of the testes. The number of each intratubular cell type as well as intertubular Leydig cells in whole samples was measured using the physical dissector counting techniques. Stereological analysis and the grids were used to determine the volume of cerebellar layers as well as the Purkinje cell number. Results: The testis weight decreased significantly in the acrylamide- treated group compared to the other groups (P<0.001). The number of spermatogonia, spermatocytes, spermatids and Leydig cells in the acrylamide-treated group were significantly less compared to the control group (P<0.05), while they were increased significantly in the acrylamide+200 mg/kg probiotic group (P<0.05; P<0.01). The mean Johnsen score in the acrylamide-treated group was lower than in the control group (P<0.001). Acrylamide-induced changes including congestion, vacuolization in the secretory epithelial cells, and epithelial rupture were observed in the prostate and seminal vesicle. The volumes of cerebellar layers were decreased in the acrylamide group compared to the control group while recovered in both probiotic treated groups. Conclusions: Probiotic microorganisms alleviate acrylamide- induced toxicities against the reproductive and cerebellar tissues in rats.