The Albert and Mary Lasker Foundation also announced Wednesday that it was giving its public service award to Planned Parenthood. Each award includes a $250,000 honorarium.
The foundation's clinical research award is shared by Dr. Douglas Lowy and John Schiller of the U.S. National Cancer Institute.
In the early 1990s they began work that would eventually lead to vaccines against human papillomavirus, or HPV, which causes cervical cancer and some other cancers.
They showed that a particular viral protein could provoke a strong immune response against the virus.
U.S. regulators approved vaccines that used their approach, called Gardasil and Cervarix, in 2006 and 2009.
By 2015, millions of women around the world had been given HPV vaccines, the foundation said. In the U.S., HPV vaccines are recommended for boys and girls.
The Lasker award for basic medical research went to Michael N. Hall of the Biozentrum Institute at the University of Basel in Switzerland.
Starting in the 1990s, he discovered and studied proteins that serve as a master regulator of cell growth, one that responds to the availability of nutrients.
Defects related to those "TOR" proteins contribute to diabetes and cancer, and scientists are developing anti-cancer drugs based on them, the foundation said.
In awarding its public service prize to Planned Parenthood, the foundation said it had provided "essential health services and reproductive care to millions of women for more than a century."
About 1 in 5 women in the U.S. has been helped by the organization at some point in their lives, the Lasker foundation said.
Besides family planning, it also provides cancer screenings and testing for sexually transmitted diseases.
The Lasker awards will be presented in New York on Sept. 15.