PIH now employs more than 13,000 people in 12 countries. Kim left the organization as Executive Director in 2003.
Kim left PIH in 2003 to join the World Health Organization (WHO) as an adviser to the director-general. In March 2004, he was appointed as director of WHO's HIV/AIDS department, after having success creating programs to fight the disease at PIH. Kim oversaw all of WHO's work related to HIV/AIDS, focusing on initiatives to help developing countries scale up their treatment, prevention, and care programs. This included an ambitious "3x5 initiative" that was designed to put three million people in developing countries on AIDS treatment by the end of 2005. The goal was not met until 2007, but according to the WHO, served to push the treatment strategy for AIDS in Africa further and faster than could have otherwise been hoped. As of 2012, the program has treated more than 7 million Africans with HIV.
Kim received a MacArthur Fellowship in 2003, was named one of America's 25 Best Leaders by US News & World Report in 2005, and in 2006 was listed as one of the top 100 most influential people in the world by Time Magazine. He serves on the Advisory Board of Incentives for Global Health, the NGO formed to develop the Health Impact Fund proposal. He is also a member of the Institute of Medicine of the United States National Academies. Kim was elected to the American Academy of Arts and Sciences in 2010.