Objective: The goal of this study was to determine what should be the specimen of choice for Chlamydia trachomatis and Mycoplasma genitalium testing in females, with focus on the sensitivity of the specimen, what women prefer and the costs of the test.Study design: Self taken vaginal swabs (SFTS) or physician taken cervical-/vaginal swab (PTCVS), and first catch urine (FCU) were collected from women visiting a STD-clinic in Oslo from 2007-2009. We collected 13 330 sample sets (11 020 PTCVS and 2310 STVS) for Chlamydia trachomatis and 13 212 sample sets (11012 PTCVS and 2201 STVS) for Mycoplasma genitalium. The samples for Chlamydia trachomatis were tested with PCR from Roche and the Mycoplasma genitalium samples was tested with an in-house PCR at Fürst laboratories. A positive diagnosis of infection was made if any of the two specimens tested positive.Results: The prevalence of Chlamydia trachomatis was 8,1 % (1077 positive), and the prevalence of Mycoplasma genitalium was 4,5 % (593 positive). For Chlamydia trachomatis the sensitivity of FCU was significantly lower than the sensitivity of SVTS and SVTS/PTCVS combined, and was slightly lower (borderline significance) compared to PTCVS alone. For Mycoplasma genitalium the sensitivity of FCU was significantly lower than SVTS, SVTS/PTCVS combined and PTCVS alone. Several studies show that SVTS is well accepted by women and that it is cost effective.Conclusion: Self taken vaginal swab is the specimen of choice when testing women for Chlamydia trachomatis and Mycoplasma genitalium in women. If the woman has symptoms a gynecological exam will be necessary and then a PTCVS will be adequate as well.