Objective To profile the omp1 genotypes of Chlamydia trachomatis (Ct) in patients with nongonococcal urethritis (cervicitis) in Guangzhou region. Methods Swab samples were obtained from the urethra of males and cervix of females in clinical settings of venereology and gynecology as well as at outreach sites for the prevention and control of sexually transmitted diseases (STDs). DNA was extracted from the swabs and nested PCR was performed to amplify the variable domain (VD) 1 - 3 of omp1 gene of Ct followed by gene sequencing. The genotypes of Ct were determined based on the amino acid mutation in VD 1 - 2 of omp1 gene. Results Totally, 1208 swabs were collected. Of them, 132 were Ct positive, and 130 positive samples underwent genotyping. Ten ompl genotypes were determined in total, including serotype E (38, 29.23%), D (25, 19.23%), J(24, 18.46%), F(21, 16.15%), G(7, 5.38%), H(5, 3.85%), K(5, 3.85%), B(2, 1.54%), Ja (2, 1.54%), I (1, 0.77%). E, D, J and F were the dominant type of Ct in this region, and amounted to 83% of all the Ct isolates. Mutations were observed within VD 1 and 2 of omp1 gene in serotype D, B and K.Serotypes were undetermined for Ct in 2 patients with mixed infection. Conclusions In Guangzhou region, E,D, F and J are the predominant genotypes of Ct, and amount to 83% of all the Ct isolates. Ct serotype B is also observed in the urethra of males and cervix of females in this region.