INTRODUCTION: Studies that compare the impact of different infectious entities of the male reproductive tract (MRT) on the male accessory gland function are controversial. MATERIAL AND METHODS: Semen analyses of 71 patients with proven infections of the MRT were compared with the results of 40 healthy non-infected volunteers. Patients were divided into 3 groups according to their diagnosis: chronic prostatitis NIH type II (n = 38), chronic epididymitis (n = 12), and chronic urethritis (n = 21). RESULTS: The bacteriological analysis revealed 9 different types of microorganisms, considered to be the etiological agents, isolated in different secretions, including: urine, expressed prostatic secretions, semen and urethral smears: E. Coli (n = 20), Klebsiella (n = 2), Proteus spp. (n = 1), Enterococcus (n = 20), Staphylococcus spp. (n = 1), M. tuberculosis (n = 2), N. gonorrhea (n = 8), Chlamydia tr. (n = 16) and, Ureaplasma urealyticum (n = 1). The infection group had significantly (p < 0.05) lower: semen volume, alpha-glucosidase, fructose, and zinc in seminal plasma and, higher pH than the control group. None of these parameters was sufficiently accurate in the ROC analysis to discriminate between infected and non-infected men. CONCLUSION: Proven bacterial infections of the MRT impact negatively on all the accessory gland function parameters evaluated in semen, suggesting impairment of the secretory capacity of the epididymis, seminal vesicles and prostate. These findings were associated with an infectious related significant increase of semen pH. None of the semen parameters evaluated can be suggested as a diagnostic tool for infection.