In 2000, Fernández was unable to run for a consecutive term as the 1994 constitution prohibited it. His party held primaries to elect a presidential nominee, which were won by Danilo Medina with 52% of the votes against Vice-President Jaime David Fernández Mirabal. Medina, who was sworn as the PLD candidate for the 2000 presidential election, was defeated by the PRD candidate, Hipólito Mejía. Mejia did not satisfy the 50% rule to avoid a feared run-off election, but Medina, who placed second, recognized Mejia's win immediately.
In 2000, Leonel Fernandez founded the Fundación Global Democracia y Desarrollo (FUNGLODE), headquartered in Santo Domingo, as a think tank as well as a resource and training center. In 2002, he founded a sister organisation, the Global Foundation for Democracy and Development, dedicated to promoting collaboration between organizations in the United States and the Dominican Republic.