We evaluated three CDC-suggested approaches for confirming positive nucleic acid amplification tests (NAATs) for Chlamydia trachomatis: (i) repeat the original test on the original specimen, (ii) retest the original specimen with a different test, and (iii) perform a different test on a duplicate specimen. For approach 1, specimens (genital swabs or first-catch urine [FCU]) initially positive by the Abbott LCx Probe System Chlamydia trachomatis Assay (LCx; Abbott Laboratories), the APTIMA Combo 2 Assay (AC2; Gen-Probe Inc.), the Amplicor CT/NG Assay (PCR; Roche Diagnostics Corp.), or the BD ProbeTec ET System C. trachomatis amplified-DNA assay (SDA; Becton Dickinson Diagnostic Systems) were retested by the same NAAT. In several evaluations, multiple efforts were made to confirm the original positive result. For approach 2, specimens initially positive by SDA and the Hybrid Capture 2 CT-ID DNA Test (HC2; Digene Corp.) were retested by different NAATs (SDA, PCR, AC2, and the APTIMA assay for C. trachomatis [ACT]). For approach 3, duplicate male urethral or cervical swabs were tested by SDA or by both AC2 and ACT. FCU specimens were tested by all three tests. We found that 84 to 98% of SDA, LCx, PCR, and AC2 positive results were confirmed by a repeat test and that 89 to 99% of SDA and AC2 and 93% of HC2 positive results were confirmed by different NAATs, but that some NAATs cannot be used to confirm other NAATs. The use of repeat testing did not confirm 11% of C. trachomatis SDA positive results that could be confirmed by more extensive testing. Doing more testing confirms more positive results; >90% of all positive NAATs could be confirmed.