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Background: Trichomonas vaginalis (T.vaginalis) and Neisseria gonorrhoeae (N.gonorrhoeae) are two most common non-viral sexually transmitted infections in the world. No data are available regarding the epidemiology of genital infections in women of Qom, central Iran. Objective: Epidemiological investigation of sexually transmitted infections in genital specimens of women referred to the referral gynecology hospital in Qom, central Iran. Materials and Methods: Genital swab specimens were collected from women volunteers and used for identification of bacterial and protozoal infections by conventional microbial diagnostics, porA pseudo gene LightCycler® real-time PCR (for N.gonorrhoeae) and ITS-PCR (for T.vaginalis). Results: Of 420 volunteers, 277 (65.9%) had genital signs/symptoms, including 38.3% malodorous discharge, 37.9% dyspareunia, and 54.8% abdominal pain. Totally, 2 isolates of Streptococcus agalactiae were identified. Five specimens (1.2%) in Thayer-Martin culture and 17 (4.1%) in real-time PCR were identified as N.gonorrhoeae. Fifty-four specimens (12.9%) in wet mount, 64 (15.2%) in Dorset’s culture, and 81 (19.3%) in ITS-PCR showed positive results for T.vaginalis. Five mixed infections of T.vaginalis+ N.gonorrhoeae were found. The risk of T.vaginalis infection was increased in women with low-birth-weight (p=0.00; OR=43.29), history of abortion (p=0.00; OR=91.84), and premature rupture of membranes (PROM) (p=0.00; OR=21.75). The probability of finding nuclear leukocytes (p=0.00; OR=43.34) in vaginal smear was higher in T.vaginalis infection. Conclusion: The significant prevalence of trichomoniasis and gonorrhea emphasizes the need for accurate diagnosis and effective surveillance to prevent serious reproductive complications in women.