BACKGROUND: Chlamydia trachomatis is common etiological agent of sexual transmitted disease. We evaluated two real-time PCR assays for the detection of C. trachomatis; Cobas TaqMan CT test v2.0 (Roche Diagnostics, Switzerland) and AdvanSure CT/NG real-time PCR (LG Life Sciences, Korea). And we compared performance of two real-time PCR assays with Cobas Amplicor CT test (Roche Diagnostics, Switzerland). METHODS: Seventy-nine cervical swab specimens collected from patients with suspected C. trachomatis infection were tested using CTM CT, ADVANSURE, and AMPLICOR for the detection of C. trachomatis. RESULTS: Twenty-five (31.6%) samples showed positive results in all three assays. The positive and negative concordance rates among three assays were 100%. CONCLUSIONS: CTM CT and ADVANSURE showed excellent agreement with AMPLICOR. Therefore, these assays were reliable for the evaluation of C. trachomatis infection.