Chlamydia trachomatis, Ureaplasma parvum, and Mycoplasma genitalium are common sexually transmitted microorganisms. Our study aimed to determine the prevalence of C. trachomatis, U. parvum, and M. genitalium in infertile and fertile couples and the effect of these microorganisms on semen parameters. In this case-control study, samples were collected from 50 infertile couples and 50 fertile couples and were subjected to the routine semen analysis and Polymerase chain reaction (PCR). C. trachomatis and U. parvum were detected in 5 (10%) and 6 (12%) of semen samples from infertile men. Also, out of 50 endocervical swabs from the infertile women, C. trachomatis and M. genitalium were detected in 7(14%) and 4 (8%) of swab specimens, respectively. In the control groups, all of the semen samples and endocervical swabs were negative. Also, in the group of infertile patients infected with C. trachomatis and U. parvum, sperm motility was lower than uninfected infertile men. The results of this study showed that C. trachomatis, U. parvum, and M. genitalium are widespread among the infertile couples in Khuzestan Province (Southwest of Iran). Also, our results showed that these infections can decrease the quality of semen. For the prevention of the consequences of these infections, we suggest a screening program for infertile couples.