Our objective was to compare the sensitivities for the detection of Chlamydia trachomatis, of the ligase chain reaction (LCR) on first voided urine (FVU) specimens and enzyme immunoassay (EIA) on pooled endocervical/endourethral swabs from women and endourethral swabs from men. Men and women taking part in the UK chlamydia screening pilot were tested for chlamydia using LCR on a FVU. Patients attending genitourinary medicine clinics also had cervical and/or urethral swabs taken for chlamydia testing by EIA. In women, EIA on pooled swabs detected 575 of the 785 chlamydia positives and in men, EIA detected 209 of 351 positives. The sensitivity of EIA was 73% and 60% in women and men respectively. By using the EIA test, therefore, 27-40% of patients infected with chlamydia will be given a false negative result. We propose that it is unethical to use non-molecular testing in the future.