The aim of this study was to evaluate the testicular lesions and their effects on the epididymal sperm parameters in the Iranian river buffalo (Bubalus bubalis). Total numbers of 117 scrota from the pubertal buffalo were provided from the local slaughterhouse. The samples were evaluated for morphological parameters and any macro- or microscopic lesions. The sterile swabs from the testis parenchyma were subjected to microbiology culture. The epididymal spermatozoon was analysed for concentration, progressive motility and abnormalities. The results showed 34.2% fibrotic adhesions between parietal and visceral layers of tunica vaginalis that was significantly different among seasons (P < 0.05). The cases of unilateral cryptorchidism and bilateral Sertoli cell tumour were detected, with no spermatozoa in the respected epididymides. Microscopic examination showed 13.25% (31/234) lesions including general (51.61%; 16/31) and multifocal (29.03%; 9/31) degenerations as well as interstitial orchitis (9.68%; 3/31) and the Sertoli cell tumour (6.45%; 2/31). No relationship between the lesions and the bacterial isolation (n = 6) was detected. The sperm parameters and morphological parameters of the testis were under influence of microscopic lesions (P < 0.05). In conclusion, the testicular macro- and microscopic lesions may have a noticeable contribution in the Iranian buffalo fertility.