Early in 1960, Rhode Island's Democratic Party asked Fogarty to run for Theodore F. Green's Senate seat when Green retired. In April, Fogarty wrote to Claiborne Pell (who would win the Senate election that fall) that he had decided to run for another term in the House instead; though the Senate would offer more prestige, greater stability, and other advantages, he said, "It is my conviction that, under present circumstances, I can serve the people of our State and Nation better by my actions as a senior member of the House rather than as a junior member of the Senate." He was right about that: during the 1960s, he sponsored an even greater expansion of medical research and health programs, along with other important social legislation.

As the Kennedy presidency began in 1961, Fogarty and his cohort were in a powerful position, having successfully broadened the scope of federal support even against Eisenhower's fiscal conservatism. And, with a Democratic president who shared their progressive goals, they expected (or hoped) that it would be easier to continue. Like many new presidents, however, Kennedy felt obliged to trim budgets and demonstrate fiscal responsibility. He was indeed more generous in his first HEW budget (for FY 1962), but Fogarty and Hill still found it inadequate and increased the appropriations considerably. Kennedy's Secretary of Health, Education, and Welfare, Abraham Ribicoff, responded by impounding $60 million of the NIH allocation, to control HEW spending. At the same time, the health coalition began experiencing backlash from other members of Congress. Although they annually documented in hearings that health research and other programs were producing results, and were an important, even vital use of tax dollars, some colleagues (Democrats and Republicans alike) just couldn't quite believe that medical research cost so much. Some observers thought that Congress was "force-feeding" the research establishment. In 1959, a House committee led by Lawrence H. Fountain (D-NC) began investigating how NIH was administering and managing the grants awarded for research at universities and non-profit organizations. It was a weak spot, as NIH director Shannon admitted. Half of the NIH budget went to such research, and NIH had grown so fast that management of its far-flung empire was rather loose. The first Fountain Committee report, in 1961, found that "the NIH was not adequately organized to administer the grant programs with maximum effectiveness," and made thirteen recommendations for improvement. Its follow-up report in 1962 was more pointed: "It appears that Congress has been overzealous in appropriating money for health research. The conclusion is inescapable, from a study of NIH's loose administrative practices, that the pressure for spending increasingly large appropriations has kept NIH from giving adequate attention to basic management problems." Fogarty and his allies responded by stepping back for several years, and actually reduced the Administration budget for NIH for FY 1964.

The Fountain Committee reports prompted President Kennedy to request a broader investigation into NIH research activities, particularly their scientific quality and value to the American public. The Wooldridge Committee started work in 1964 (delayed by Kennedy's death in late 1963), visiting over 600 NIH grant recipients and 150 institutional administrators. They were aided by 77 scientists and administrators in gathering and evaluating data on the projects. The committee's 1965 report concluded that in general "the activities of the NIH are essentially sound and that its budget of approximately one billion dollars a year is, on the whole, being spent wisely and well in the public interest." It did, however, agree that the organization and procedures needed strengthening, and made recommendations for changes. The constraints imposed on HEW budgets by the investigations were uncomfortable, but temporary. NIH continued to grow, adding two new institutes--General Medical Sciences and Child Health and Human Development--in 1963. The NIH budget for 1966 topped $1 billion. It would never again grow as fast as it had between 1956 and 1963.

Besides maintaining generous annual increases to the NIH appropriations, Fogarty introduced other important legislation between 1961 and 1964. The 1963 Maternal and Child Health and Mental Retardation Planning Amendments to the Social Security Act authorized a five-year $265 million program to provide child and maternal health services, health care for expectant mothers at risk for problem pregnancies, funds for research to improve maternal and child health and crippled children's services, and grants to states to help in developing plans for state and community programs to combat mental retardation. A companion measure, the Mental Retardation Facilities and Community Mental Health Centers Construction Act, provided $329 million over five years to assist in the construction of mental retardation research centers and community mental health centers, and to train teachers of mentally retarded and other handicapped children. Congress also extended the Hill-Burton Hospital Construction Act for five years, and a program of public health traineeships and training grants to schools of public health, nursing, and engineering. The Library Services and Construction Act of 1964 expanded the original act to include urban as well as rural communities.

The 1964 election gave the Democrats a very strong majority in both House and Senate, and kept Lyndon Johnson in the White House. With a much more liberal Congress, much of the legislation on Johnson's Great Society agenda (which included civil rights, education, health care and other social programs) was passed. Many Fogarty-sponsored bills were part of the legislative deluge: the National Technical Institute for the Deaf Act of 1965 authorized the establishment of the institute at the Rochester Institute of Technology in 1968; the Mental Retardation Facilities and Community Mental Health Centers Construction Act Amendments of 1965 helped finance initial staffing of community mental health centers, and increased funding of mental retardation education research and training teachers for handicapped children; the Health Research Facilities Amendments of 1965 extended the program for construction of health research facilities for three years; the Heart Disease, Cancer, and Stroke Amendments of 1965 provided for establishment of regional cooperative programs in research, training, continuing education and demonstration activities in patient care among medical schools, clinical research institutions and hospitals, so that the latest treatments for those diseases could be more widely available. The Medical Library Assistance Act of 1965 authorized the National Library of Medicine to award extramural grants and to establish the Regional Medical Libraries. Fogarty also supported plans for the establishment of a research center in biomedical communications at NLM, though he didn't live to see this carried out.

Fogarty was also the original sponsor (starting in 1963) for the 1965 National Foundation on Arts and Humanities Act, which created the National Endowment for the Arts and National Endowment for the Humanities. Likewise, he had been one of the original sponsors of the Older Americans Act of 1965. Fogarty also was instrumental in the enactment of the Manpower Development and Training Act of 1965 and the Economic Opportunity Amendments of 1965, and he strongly supported Johnson's Medicare and Medicaid legislation. During his last term in Congress, he was working on legislation for a program ("Preventicare") that would provide a range of health tests for all Americans age fifty and over, to screen for chronic diseases, and Social Security Act amendments that would extend child welfare services.

Ironically, Fogarty, who was known for his kind heart and his courage, and who had done so much to support research on heart disease, died of a heart attack on January 10, 1967. His funeral in Providence drew huge crowds, and many members of Congress praised him at a memorial service in the House. Silvio O. Conte (R-MA) offered one of the tributes: "[John Fogarty] met his responsibilities with an immense vitality, a penetrating insight, and a keen understanding of the problems at hand. He obtained results by tempering this with an equally firm grasp of both the capacities and limitations of our power to solve these problems. He was a relentless worker, but a quiet and self-effacing one as well. He would deny the immense impact of his achievements while others, including his own President, would applaud and honor him."

Fogarty's death was the beginning of the end of the health coalition; Lister Hill retired from the Senate and James Shannon retired from NIH the following year. Melvin Laird left the Congress when he was appointed Secretary of Defense in 1969. Mary Lasker had increasingly alienated her allies by pressing for projects that would produce medical "payoffs," especially for cancer. Competing priorities, especially the Vietnam War, made it difficult to maintain the expansion of public health and research projects, and some of the ambitious 1960s programs were eventually scrapped. Nevertheless, much of Fogarty's life work endures, particularly at the National Institutes of Health, and in the many programs for the most vulnerable Americans.