The Biomarkers Study, short for “Characterisation of Novel Microbicide Safety Biomarkers in East and South Africa”, was initiated with the overall aim of establishing baseline ranges of biomarkers related to the vaginal environment in African target populations for microbicide trials. Funded by European and Developing Countries Clinical Trials Partnership (EDCTP), this was a multi-centre trial with sites in Kenya (ICRH), Tanzania (MITU/NIMR), Rwanda (Projet Ubuzima) and South Africa (RHRU). The study was initi- ated at Mombasa, the Kenyan site and the subject of this report, in November 2010 with the mandate to enroll 170 HIV-negative female participants i.e.: 30 adolescents, 30 pregnant and 110 non-pregnant adults.