Background: Although teenage pregnancies in South Africa have declined, the short and longer term health and social consequences are a potential public health concern. This longitudinal study aimed to describe the range of risk and protective factors for incident unwanted and unplanned pregnancies occurring over 2 years of follow-up among a cohort of adolescent women in the Eastern Cape, South Africa. It also investigated the relationship between gender inequality and gender-based violence and subsequent unplanned and unwanted pregnancies among the cohort.