The distribution of different Chlamydia trachomatis serovars in Hungary has not been reported previously. The objective of this study was to determine the distribution and prevalence of C. trachomatis serovars in a high-risk population by genotyping. The endocervical specimens of 484 female sex workers (FSWs) were screened for C. trachomatis by plasmid PCR. Genotyping was performed in all C. trachomatis-positive samples by PCR-based RFLP analysis of the omp1 gene. A total of 32 specimens (6.6 %) were positive for C. trachomatis. Age was an important risk factor for C. trachomatis infection in FSWs. The highest prevalence was detected in women under the age of 20 (18.8 %). All positive specimens were successfully genotyped and seven serovars were identified. The most prevalent was serovar D (34.4 %), followed by E (21.9 %), F (18.8 %), G (9.4 %), J (9.4 %), H (3.1 %) and I (3.1 %). A heterogeneous distribution of C. trachomatis serovars was observed in the study group, where the most common serovars were D, E and F comprising 75 % of the positive samples. This PCR-based RFLP method could be used in epidemiological studies on the prevalence of C. trachomatis infection to provide more information and to compare the serovar distribution among different cohorts.