A plasmid-based PCR for the detection of Chlamydia trachomatis was evaluated with a confirmatory PCR employing a second set of plasmid primers. A total of 258 genitourinary specimens including 134 female endocervical and urethral specimens and 124 male urethral specimens were tested by culture, blocked EIA and PCR. Fifty-four specimens were positive by culture, 50 were positive by EIA and 71 were positive by PCR. Fourteen specimens that were PCR-positive but culture- and EIA-negative were confirmed positive by the confirmatory PCR. Two of the 187 specimens which were negative by culture and EIA were positive by PCR but failed to confirm with the second set of primers. Using an expanded gold standard of culture, blocked EIA and confirmed PCR, the overall sensitivities for culture, blocked EIA and confirmed PCR were 76.0% (54/71), 70.4% (50/71) and 100% (71/71) and the specificities were 100% (187/187), 100% (187/187), respectively. These results demonstrated that a confirmatory PCR was useful for sorting out discordant specimens and establishing the true specificity of PCR. Furthermore, these results demonstrate that PCR is more sensitive than culture and EIA and suggest that a confirmed PCR test should be included in the gold standard for the evaluation of new tests for diagnosing Chlamydia trachomatis infections.