The Gates Foundation funds programs to improve mother and child health and to combat infectious diseases. Looking at "Partners" for each program will lead you to other NGOs.
Founded to was founded to "help save the lives of millions of people living with HIV/AIDS in the developing world by dramatically scaling up antiretroviral treatment", CHAI also has programs in maternal, newborn and child health, malaria, and vaccines.
GAVI = Global Alliance for Vaccines and Immunisation, a public-private partnership aiming to increase equitable use of vaccines in lower-income countries
PIH works to provide a preferential option for the poor in health care, by establishing long-term relationships with sister organizations based in settings of poverty and working in close partnership with local government officials and the world’s leading medical and academic institutions.
An international nonprofit organization with the aim of improving health through accelerating innovation in 5 areas: vaccines, drugs, diagnostics, devices, and systems and service innovations.
This search page at Find Policy, still experimental, focuses on research organizations that work on Global Health. In addition to institutions focusing on decreasing global inequity in health, this engine also includes institutions with a focus on global health policy issues. US institutions are included to the extent that they do extensive international work.