MTN conducts its multi-center studies through NIH-funded clinical trial units (CTUs) with sites in Malawi, South Africa, Uganda, Zambia, Zimbabwe, India and the United States. CTUs based outside the United States are the National AIDS Research Institute in Pune, India; the Medical Research Council in Durban, South Africa (with four sites); Centre for the AIDS Programme of Research of South Africa (CAPRISA) in Durban, South Africa; and the University of Cape Town, South Africa.

Other international sites participate in MTN trials through collaborations with U.S.-based CTUs. These include two sites each in Zimbabwe (University of California, San Francisco) and Malawi (Johns Hopkins Bloomberg School of Public Health); and one site each in Uganda (Johns Hopkins School of Medicine) and Zambia (University of Alabama at Birmingham). The remaining U.S.-based CTUs are Case Western Reserve University in Cleveland; Columbia University in New York City, the University of Pittsburgh; the University of Pennsylvania, Philadelphia; and the University of Alabama at Birmingham, which is separate from its international site.

MTN also conducts studies at the University of South Florida in Tampa and the University of Puerto Rico in San Juan through a collaboration with the Adolescent Medicine Trials Network for HIV/AIDS Interventions (ATN) of the National Institute of Child Health and Human Development.