Background: Pregnancy is associated with complications which must be differentiated from adverse events associated with the administration of vaccines during pregnancy both in clinical trials and post licensure surveillance. The frequency of pregnancy related complications varies significantly by geographical location and the prevalence of pregnancy and neonatal outcomes are poorly documented in most low-resource settings. In preparation for Group B Streptococcus maternal vaccination trials, we describe a protocol for a pregnancy register at Kawempe National Referral Hospital, Kampala, Uganda to describe pregnancy maternal and infant outcomes. Methods: The study has two components. Firstly, an active, prospective surveillance cohort consisting of pregnant women in their first or second trimester recruited and followed up through their hospital scheduled antenatal visits, delivery and their infants through their extended programme of immunisation visits until 14 weeks of age. Data on obstetric and neonatal outcomes defined by the Brighton Collaboration Global Alliance of Immunisation Safety Assessment in Pregnancy criteria will be collected. Secondly, a passive surveillance cohort collecting data through routine electronic health records on all women and infants attending care at KNRH. Data will be collected on vaccinations and medications including antiretroviral therapy received in antenatal clinic and prior to hospital discharge. Discussion: Conducting vaccine research in resource-limited settings is essential for equity and to answer priority safety questions specific to these settings. It requires improved vaccine safety monitoring, which is especially pertinent in maternal vaccine research. During a trial, understanding the epidemiology and background rates of adverse events in the study population is essential to establish thresholds which indicate a safety signal. These data need to be systematically and reliably collected. This study will describe rates of adverse pregnancy outcomes in a cohort of 4,000 women and infants and any associated medications or vaccines received at a new vaccine trial site in Uganda.