The aim of this study was to compare culture and polymerase chain reaction techniques in detection of Chlamydia trachomatis in clinical specimens. Two hundred clinical specimens previously examined for C. trachomatis by culture were analysed blindly by polymerase chain reaction. A 144 bp fragment of DNA from the MOMP of C. trachomatis was amplified. In addition, a 250 bp segment of beta-globin gene was amplified as an internal control. In 27 culture negative specimens, the beta-globin amplicon was not detected. Of the 173 specimens assessable by PCR, 24 (13.8%) were positive by both methods. Four specimens were positive by PCR and negative by culture. Three were collected post-antibiotic treatment; two were from previous culture-proven chlamydia infection suggestive of the presence of DNA of non-viable organisms, and one case was toxic by culture. No specimen was positive by culture and negative by PCR. Overall PCR when compared to culture had a sensitivity of 100% and specificity of 97.3% with positive and negative predictive values of 85.7% and 100%, respectively. PCR is especially useful when culture results can not be confirmed due to toxicity, inadequate transport or insufficient specimen collected.