Discrepant analysis is a widely used technique that attempts to provide estimates of sensitivity and specificity in the presence of an imperfect gold-standard. This technique has been applied by many researchers to estimate the sensitivity and specificity of DNA-amplification tests for Chlamydia trachomatis such as the plasmid-based ligase chain-reaction and polymerase chain-reaction tests. However, the sensitivity and specificity estimates obtained by discrepant analysis are upwardly biased, and this bias remains even when a perfect test is used to resolve the discrepant results. This technique should not be adopted for evaluating the performance of a diagnostic test.