Background While most Sub-Saharan African countries are now implementing the WHO-recommended Option B+ protocol for prevention of vertical HIV transmission, there is a lack of knowledge regarding the influence of Option B+ exposure on adverse birth outcomes (ABOs). Against this background, we assessed ABOs among delivering women in Western Uganda. Methods A cross- sectional, observational study was performed within a cohort of 412 mother- newborn-pairs in Virika Hospital, Fort Portal in 2013. The occurrence of stillbirth, pre-term delivery, and small size for gestational age (SGA) was analysed, looking for influencing factors related to HIV-status, antiretroviral drug exposure and duration, and other sociodemographic and clinical parameters. Results Among 302 HIV-negative and 110 HIV-positive women, ABOs occurred in 40.5%, with stillbirth in 6.3%, pre-term delivery in 28.6%, and SGA in 12.2% of deliveries. For Option B+ intake (n = 59), no significant association was found with stillbirth (OR 0.48, p = 0.55), pre- term delivery (OR 0.97, p = 0.92) and SGA (OR 1.5, p = 0.3) compared to seronegative women. Women enrolled on antiretroviral therapy (ART) before conception (n = 38) had no different risk for ABOs than women on Option B+ or HIV-negative women. Identified risk factors for stillbirth included lack of formal education, poor socio-economic status, long travel distance, hypertension and anaemia. Pre-term delivery risk was increased with poor socio-economic status, primiparity, Malaria and anaemia. The occurrence of SGA was influenced by older age and Malaria. Conclusion In our study, women on Option B+ showed no difference in ABOs compared to HIV-negative women and to women on ART. We identified several non-HIV/ART-related influencing factors, suggesting an urgent need for improving early risk assessment mechanisms in antenatal care through better screening and triage systems. Our results are encouraging with regard to continued universal scale-up of Option B+ and ART programmes.