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There is an increasing reliance on noninvasive techniques to collect specimens for the detection of sexually transmitted infections. The acceptability of these methods among the general population has been explored, but little is known about their acceptability among women confined in prison.The goal was to compare female prisoners’ preferences for collection of specimens (self-collected vaginal swab specimens, urine collection, or pelvic examination) for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.A cross-section of inmates in a large federal prison provided urine samples and self-collected vaginal swab specimens. Women then completed a questionnaire regarding the ease of each method and their preferences for future specimen collection.A total of 535 women between the ages of 18 and 52 years (median = 33) participated in the study. More than half of the participants (57%) reported no difference between urine and swab in terms of ease of collection. Approximately 30% of participants said they would prefer to give a swab specimen in the future rather than collect urine (21%), but nearly half of the women expressed no preference for one method over the other. Most participants (60%) expressed a preference for providing a self-collected swab specimen rather than having a pelvic examination (23%), but nearly 17% expressed a preference for one over the other.The study population of female federal prisoners expressed no aversion to the self-collection of either vaginal swab or urine specimens for STD testing. A majority of participants expressed a preference for noninvasive techniques rather than a pelvic examination.