In 1958, Dooley co-founded MEDICO and helped establish seventeen medical programs in fourteen countries. The purpose of MEDICO was to be a person-to-person program. MEDICO aided the sick and taught the people in third world countries to care for themselves and each other. While in Muong Sing, Dooley, Rhine, and Davis usually treated over 100 people per day. Dooley and MEDICO established hospitals and trained the local people, and eventually, MEDICO turned the hospitals over to the local people and government.

          Dooley also used some of MEDICO's money to send young Laotians to study in the United States. One of these students was Ngoan Van Hoang. In June 1960, Dooley dictated an encouraging letter to Hoang. Dooley was proud of Hoang's report card and encouraged him to remember where he came from.

          After Dooley's death, MEDICO tried to continue its support of various hospitals around the world, including Laos, Cambodia, Hong Kong, Thailand, and Burma. However, without Dooley's fund-raising, contributions decreased. MEDICO was forced to close some hospitals later in 1961. Then in March 1962, MEDICO was absorbed by the organization CARE, Cooperative for Assistance and Relief Everywhere, Inc. CARE is one of the world's largest private international relief and development organizations, founded in the aftermath of World War II. CARE continues to provide humanitarian aid to families and communities in times of crisis.

          Dr. Verne Chaney, Teresa Gallagher, Agnes and Malcolm Dooley, and others from MEDICO felt that Dr. Peter Comanduras and MEDICO were not following Dooley's plans for the organization. In September 1961, Dr. Chaney helped found the Thomas A. Dooley Foundation as a non-profit, non-sectarian, non-government, non-political, private, and voluntary organization dedicated to the memory of Dr. Tom Dooley and his pioneering work. The Foundation reopened a former MEDICO hospital in Laos, assisted the An Lac orphanage in Saigon, conducted a health survey of Nepal, and arranged for boats to travel the Mekong River and give medical aid to people along the river.

          In 1976, the Foundation became the Thomas A. Dooley Foundation-INTERMED, Inc. Fundraising in the United States is done by the Dooley Foundation, and all projects outside the country are managed by INTERMED, Inc. The organization continues to collaborate with World Medical Relief and the Air Commando Association to provide preventive medicine, health education, training, care for the sick, immunizations, research, and more.

          In the summer of 1970, Teresa Gallagher and other members of the Thomas A. Dooley Foundation established the Tom Dooley Heritage to carry on Dooley's work with the help of volunteers. They built and maintained the Tom Dooley Hospital in Thailand to provide medical care to Thai and Laotian refugees and to teach them to care for themselves. The foundation also held memorial services for Dooley each year.