This study was aimed to investigate the long-term effect of vasectomy using the bonnet monkey (Macaca radiata) as a primate animal model. Animals weighing around 6 to 8 kg were randomly chosen for bilateral, unilateral vasectomy and sham-control. The postoperative periods of six months and two years were considered as short and long-term, respectively. Sperm were collected and subjected to analysis before euthanasia. The testes and epididymides were excised from euthanized animals then embedded in paraffin. Normal histological changes were observed in sham-operated animals and short-term contralateral testes. In contrast, marked alterations were observed in the testes and epididymides of both short and long-term groups. Seminiferous epithelium was thinned out showing marked depletion of germ cells in long-term; only a thin layer of Sertoli cells, spermatogonia, and fewer spermatocytes were seen. Exfoliation of germ cells and the occurrence of multinucleated giant cells were common features in these tubules. The epididymal tubular lumens were greatly dilated with accumulated spermatozoa in short and long-term animals; significant defects were observed in the epithelium of the long-term animals. Microscopic spermatic granulomas were noticed in epididymides and the vas deferens. Large granulomas were seen in long-term vasectomized monkeys, frequently compressing the surrounding structures. These granulomas could be visualized in ultrasound, however, only at the late stage of its occurrence. Sperm collected from the unilateral vasectomized animals showed a poor motility score in the capillary mucus penetration test (CMPT). Results indicate that the changes observed after vasectomy might be due to pressure initially, whereas in the long-term the damage was supplemented by autoimmune attack. With immunoglobulin (IgG) deposition in contra-lateral unoperated testis of unilateral vasectomized animals it also showed degenerative changes and a concomitant drop in sperm quality. Although, granulomatous reactions were observed in the epididymis and vas deferens but testes were spared from such reactions even in the long-term.