Chlamydia trachomatis infection is considered the most prevalent bacterial sexually transmitted disease worldwide. C.trachomatis causes eye infections such as trachoma and newborn inclusion conjunctivitis, newborn pneumonia, genitourinary system infections and suppurative inguinal lymphadenitis namely lymphogranuloma venerum. The aim of this study was to investigate C.trachomatis by direct fluorescent antibody (DFA), polymerase chain reaction (PCR) and cell culture methods in the clinical samples sent to the microbiology laboratory with the prediagnosis of genital infections. A total of 50 swab samples obtained from adult patients (49 female, 1 male) who were admitted to Erciyes University Hospital, Kayseri, Turkey between February-March 2010, were included in the study. C.trachomatis antigens were investigated by a commercial DFA (PathoDx, Remel, USA) method. McCoy cell cultures prepared in microplate wells were used for the isolation of C.trachomatis. The growth of C.trachomatis in cell cultures was confirmed by DFA and iodine staining methods. C.trachomatis DNA was investigated by commercially available PCR (Chlamydia trachomatis 330/740 IC; Sacace, Italy) method. In our study, 4 (8%) of the 50 swab samples were found positive with DFA, 1 (2%) was positive with cell culture, and 1 (2%) was positive with PCR. The only sample that gave positive results with all of the three methods was an urethral swab. Three cervical swab samples that were found positive only with DFA method was evaluated as false positivity. When cell culture was considered as the reference method, the sensitivity and specificity of DFA method were estimated as 100% and 94%, respectively, while those rates for PCR were 100% and 100%, respectively. In conclusion, although cell culture is still the gold standard in the diagnosis of C.trachomatis. infections, since it is time consuming and difficult to apply, more rapid and reliable PCR methods may be applied in diagnosis. DFA method which is practical and cheap, is preferred largely in routine laboratory practice. However, false negative and false positive DFA results should be prevented by the maintainence of good quality clinical specimens, evaluation of the test by experienced personnel and use of quality control samples in each run.