Vaginal swab specimens may be preferable to cervical swab or urine specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae because of the ease of specimen collection and transport. The purpose of this study was to evaluate whether vaginal swab specimens are equivalent to cervical swab specimens for the detection of N. gonorrhoeae and C. trachomatis by the Becton Dickinson strand displacement amplification assay (SDA) with the BDProbeTec ET instrument and then to evaluate the use of the amplification control in a clinical research setting. In the first phase, vaginal and cervical swab specimens were obtained from 455 symptomatic women aged 18 to 40 attending primary health care and sexually transmitted disease clinics. Thirty-nine specimens (8.6%) had true-positive results for N. gonorrhoeae and 37 specimens (8.6%) had true-positive results for C. trachomatis. The sensitivity of SDA was superior to that of culture for the detection of C. of N. gonorrhoeae with vaginal swab specimens and equivalent to that of the Roche PCR for the detection of C. trachomatis with cervical swab specimens. In the second phase of the study, 1,411 consecutively collected vaginal swab specimens were evaluated, with 357 (25.3%) specimens giving indeterminate readings on the basis of the result for the amplification control. The prevalences of sexually transmitted pathogens in vaginal swab specimens with and without use of the amplification control were 6.0 and 5.8%, respectively, for C. trachomatis and 3.1 and 3.0%, respectively, for N. gonorrhoeae. Although, vaginal swab specimens were equivalent to cervical swab specimens for the detection of N. gonorrhoeae and C. trachomatis by SDA with respect to sensitivity, one in four vaginal swab specimens yielded an indeterminate result when the amplification control was used. The amplification control has limited value for use with vaginal swab specimens.