Objective: We evaluated agreement in diagnoses for bacterial vaginosis (BV), Trichomonas vaginalis (TV) and vulvovaginal candidiasis (VVC) between clinicians examining the patient and performing diagnostic tests versus a clinician with access only to the patient's history and diagnostic findings from self-obtained vaginal swabs (SOVS). Design: Women presenting with vaginal discharge to a sexually transmitted infections clinic provided SOVS for evaluation and completed the study and qualitative questionnaires. A clinician then obtained a history and performed speculum and bimanual examinations. Participants' history and diagnostic test results from SOVS were provided to a masked non-examining clinician who rendered independent diagnoses. Overall agreement in diagnoses and κ statistics was calculated. Results: The prevalence of infections among the 197 participants was 63.4% (BV), 19% (TV) and 14% (VVC). The per cent agreement between the examining and non-examining clinician for the diagnoses of BV was 68.5%, 90.9% for TV and 91.9% for VVC. Of the 105 women diagnosed with BV by the examining clinician, 34 (32%) were missed by the non-examining clinician. The non-examining clinician missed 13 (48%) of 27 women and 12 (34%) of 35 women treated for VVC and TV, respectively. Four women who all presented with abdominal pain were diagnosed with pelvic inflammatory disease. Conclusions: Tests from SOVS and history alone cannot be used to adequately diagnose BV, TV and VVC in women presenting with symptomatic vaginal discharge. Cost benefits from eliminating the speculum examination and using only tests from SOVS may be negated by longterm costs of mistreatment.