After vasectomy (VAX), the flux and composition of the epididymal fluid are modified, leading to sequelae to the epididymis. In an effort to understand molecular pathophysiology of the epididymis following VAX, we investigated the changes of gene expression and sperm functions in the epididymis of vasectomized mice. After VAX, the epithelial cell height was significantly decreased in cauda epididymis, resembling the those of vas deference. This suggests that VAX evokes alteration of segmental characteristics of epididymal epithelium. Of note, these was an increase in luminal diameter in corpus and cauda epididymis, indicating the alteration of fluid homeostasis in epididymal lumen and protein synthesis and secretion. Also, the formation of sperm granuloma and infiltration of inflammatory cells were noted in lumen of epididymis at 8 weeks postvasectomy, indicating the activation of immune response in epididymis. The serum TNF-α levels and epididymal TNF-α and IL-1β mRNA levels were significantly increased in VAX mice. Microarray analysis demonstrated that claudin (CLDN) 10 and cystic fibrosis transmembrane conductance regulator (CFTR) were downregulated after vasectomy. In contrast, angiotensin II receptor type 2 (Agtr2) was up-regulated after vasectomy. Taking into account the functional importance of angiotensin system in epididymal epithelia and muscle tissue, VAX may alter the secretory function of epithelia and sperm transport via alteration in angiotensin system. Importantly, the IgG type of anti-sperm antibody (ASA) were markedly increased in the blood of vasectomized mice. Together this indicates that VAX provokes local inflammation in epididymis as well as systemic inflammation, which in turn change the blood epididymal barrier, an important element for epididymal immunological privilege. In addition, the number of sperm in cauda epididymis was increased but the sperm motility was decreased after vasectomy. The spontaneous acrosome reaction was increased by vasectomy after capacitation. This suggests that VAX affects sperm functions as well as sperm maturation. In conclusion, bilateral vasectomy lead to local immune response of epididymis, causing immunologic infertility in men.