Trichomoniasis is the most prevalent non-viral sexually transmitted infection worldwide. It has been estimated that 276 million new infections occurred in 2008 with 11.5% increase over the 2005 incidence rate [1]. Worldwide, the estimated prevalence rates vary with geographic location, age, race, community and the method used for diagnosis. In 2016, the WHO global estimate for trichomoniasis in women was estimated at 5.3% and 0.6% in men with a total incidence of 156 million cases [2]. In Egypt, a prevalence rate of 8.0% was recently documented among symptomatic women in Beni Suef Governorate [3] ; in addition to 11% in Benha, Qalyubia Governorate [4] , and 5% in Cairo [5]. Another older study recorded prevalence rate of 27-57% using different techniques for diagnosing trichomoniasis in Shebin El-Kom, Menoufia Governorate [6]. While infections are mostly asymptomatic in men, women usually present with vaginal discharge, pruritus and dysuria [7,8]. Trichomoniasis is considered an important risk factor for herpes simplex virus type II infections and HIV transmission and acquisition [9,10]. Data from studies in Africa recorded an increase in HIV transmission associated with trichomoniasis [11-13]. In an American study, the investigators detected T. vaginalis in 20% of HIV-infected pregnant women using PCR assay [14]. Moreover, it may be associated with cervical cytological abnormalities and cervical cancer [15-18]. Such a difference in clinical traits as virulence, pathogenicity and drug resistance, signifies the need to link phenotypic variation to genotype [19]. In Egypt, former attempts to investigate the diversity of T. vaginalis included isoenzyme patterns [20] , serotyping [21] , immunoblotting [22,23] , biological variability [24,25] and HSP70-RFLP [26]. These studies concluded that the different clinical isolates have different and common patterns at the levels of antigens, immunogens, pathogenicity and MTZ resistance. Molecular typing methods revealed a two-type population structure for T. vaginalis, type I and type II [27-31]. Genotype I infections were found to have lower probability of associated discolored discharge, especially bloody discharge, bleeding during physical examination, or presence of greater than 20% clue cells. Infections with genotype II were significantly associated with these pathological findings. The increase in clue cells seen with genotype II are indicative of bacterial vaginosis, providing a change in the vaginal microenvironment that is favorable for infection with other microbial pathogens. Genetic diversity for T.