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Background: In sub-Saharan Africa (SSA) there are strong arguments for the provision of integrated sexual and reproductive health (SRH) and HIV services. Most HIV transmissions are sexually transmitted or associated with pregnancy, childbirth, and breastfeeding. Many of the behaviours that prevent HIV transmission also prevent sexually transmitted infections and unintended pregnancies. There is potential for integration to increase the coverage of HIV services, as individuals who use SRH services can benefit from HIV services and vice-versa, as well as increase cost-savings. However, there is a dearth of empirical evidence on effective models for integrating HIV/SRH services. The need for robust evidence led a consortium of three organizations - International Planned Parenthood Federation, Population Council and the London School of Hygiene & Tropical Medicine - to design/implement the Integra Initiative. Integra seeks to generate rigorous evidence on the feasibility, effectiveness, cost and impact of different models for delivering integrated HIV/SRH services in high and medium HIV prevalence settings in SSA., Methods/design: A quasi-experimental study will be conducted in government clinics in Kenya and Swaziland - assigned into intervention/comparison groups. Two models of service delivery are investigated: integrating HIV care/treatment into 1) family planning and 2) postnatal care. A full economic-costing will be used to assess the costs of different components of service provision, and the determinants of variations in unit costs across facilities/service models. Health facility assessments will be conducted at four time-periods to track changes in quality of care and utilization over time. A two-year cohort study of family planning/postnatal clients will assess the effect of integration on individual outcomes, including use of SRH services, HIV status (known/unknown) and pregnancy (planned/unintended). Household surveys within some of the study facilities' catchment areas will be conducted to profile users/non-users of integrated services and demand/receipt of integrated services, before-and-after the intervention. Qualitative research will be conducted to complement the quantitative component at different time points. Integra takes an embedded 'programme science' approach to maximize the uptake of findings into policy/practice., Discussion: Integra addresses existing evidence gaps in the integration evaluation literature, building on the limited evidence from SSA and the expertise of its research partners., Trial Registration: Current Controlled Trials NCT01694862.