BACKGROUND Trichomoniasis is an extremely common sexually transmitted infection (STI) worldwide and is associated with important public health problems, including amplification of HIV transmission. This disease is in forms of symptomatic and asymptomatic in women and may depend on host as well as parasite variables. Most of the studies reported from females are based on examination of vaginal secretions and urine samples by direct smear and culture in modified Diamond's media. The aim of this study was checking the samples, which were negative by direct smear and culture, with PCR technique. METHODS The urine samples and vaginal discharge of patients attending Gynecology Clinics of Mazandaran Province, Iran with different symptoms rechecked for Trichomonas vaginalis by PCR technique using primers targeting a conserved region of the beta-tubulin genes of the parasite. Data were analyzed by Epi Info software program RESULTS Out of 161 negative samples by direct smear and culture, seven samples (4.3%) were positive by PCR technique. CONCLUSIONS Diagnosis of trichomoniasis by PCR is a sensitive and specific method that could play important role to help the physicians for properly treatment and control of infection.