OBJECTIVE: To measure the frequencies of sexually transmitted infections (STIs) and adverse pregnancy outcomes among women receiving either aetiological testing or syndromic management for STIs. DESIGN: Non-randomised prospective cohort study. SETTING: Primary healthcare facilities in Tshwane, South Africa. POPULATION: HIV-infected pregnant women attending antenatal care services. METHODS: Participants were enrolled to receive aetiological testing using Xpert CT/NG and Xpert TV assays or standard syndromic management. Outcome data were collected at the postnatal care visit (≤30 days from delivery) and from maternity records. Enrolment gestational age-adjusted relative risk (aRR) was calculated. MAIN OUTCOME MEASURES: STI prevalence at postnatal visit, and frequency of adverse pregnancy outcomes (preterm birth, low birthweight). RESULTS: We enrolled 841 women. The prevalence of any STI at baseline was 40%; Chlamydia trachomatis 30%, Neisseria gonorrhoeae 5.6%, Trichomonas vaginalis 20%. The prevalence of STIs at postnatal care was lower among those receiving aetiological testing compared with those receiving syndromic management (14% versus 23%; aRR 0.61; 95% CI 0.35–1.05). No difference was observed between study groups for frequency of preterm birth (23% versus 23%; aRR 1.2, 95% CI 0.81–1.8) and low birth weight (15% versus 13%; aRR 1.1, 95% CI 0.66–1.7). CONCLUSIONS: Aetiological testing provides an effective intervention to reduce the high burden of STIs in pregnant women in South Africa; however, the optimal implementation strategy remains to be determined.