AIMS: To compare ELISA and Southern blot hybridisation for the detection of PCR amplified Chlamydia trachomatis DNA extracted from clinical samples; to assess the value of the ELISA method in a clinical setting. METHODS: DNA was extracted from urogenital samples of 508 patients, purified and amplified using C trachomatis specific primers, one of which was endlabelled with biotin. Amplification products were detected by Streptavidin biotin based ELISA and non-radioactive Southern blotting. RESULTS: Of the 508 samples, 29 were positive and 479 negative by both methods. No discrepant results were observed. CONCLUSION: Streptavidin biotin based ELISA and Southern blotting were equally sensitive for detecting PCR amplified C trachomatis DNA. Using ELISA, test results could be generated within a single day.