The purpose of this study was to detect the presence of HHV-6 A and HHV-6 B in genital samples of infertile men, relating these findings to alterations of normal seminal parameters, considering only those samples in which there was no co-infection with other frequent genital tract microorganisms such as Chlamydia trachomatis, Human Papillomavirus, and Herpes Simplex Virus 1 and 2. For these assays, were processed 105 semen and urethral swab samples from men with a diagnosis of infertility. Seminal parameters were determined for each of them and subsequently molecular biology tests were performed to detect DNA for HHV-6 A, HHV-6 B, HSV, HPV, and Chlamydia trachomatis Of the total samples processed, 28.5% (30/105) were positive for HHV-6 A/B of which 23.3% (7/30) corresponded to HHV-6 A and 76.7% (23/30) corresponded to HHV-6 B. No HHV-6 A and B coinfection was detected. HHV-6A co-infected with any of the pathogens studied in 14.2% samples (1/7) while HHV-6B co-infected in 26.1% samples (6/23). The odds ratio obtained was 1.44, reflecting a positive association. Statistically significant differences were observed between HHV-6 A and B when volume and morphology parameters were analyzed. Both HHV-6A and HHV-6B are associated with alterations in sperm volume, concentration, motility, mortality and morphology. The presence of HHV-6B in genital samples would be associated with alterations in sperm volume and morphology, but their true pathological role, still remains to be answered.