This study was designed to determine the prevalence and distribution of Chlamydia trachomatis genotypes from clinical specimens in Guangzhou, China, obtained in the period 2005-2008. One hundred and ninety-four urogenital C. trachomatis samples were collected from sexually transmitted disease clinic patients, and the VS1-VS2 of OmpA gene was amplified by nested PCR and sequenced using an ABI-prism 3730 sequencer. Clinical C. trachomatis strains were genotyped and analyzed for a mutation with respect to the reference VS1-VS2 sequence. VS1-VS2 fragments with 453 bp were amplified from 194 clinical samples. Upon alignment with the sequences of the reference strains, 189 strains with discernible sequences were typed into 9 genotypes, while 5 with ambiguous sequences were considered to be mixed-serovar samples. The most prevalent genotypes were E (50, 26%), F (46, 24%), J (35, 19%), and D (24, 13%). There was no significant difference in the distribution of any of the genotypes detected during the study period, except for genotype K (P<0.01). A total of 16 (8%, 16/189) genetic variants of the OmpA VS1-VS2 of the reference strains were identified. Mutations occurred frequently for genotypes D (2/24, 8%), E (6/50, 12%), F (2/46, 4%), G (1/8, 13%), H (1/12, 8%), and K (4/11, 36%), with most of these being sense mutations that may result in amino acid substitution. Sequencing the OmpA VS1-VS2 enabled the genotype and sequence variations within each genotype to be analyzed. Genotypes E, F, J, and D continued to dominate among urogenital C. trachomatis, whereas genotype K increased significantly in Guangzhou between 2005 and 2008.