The prison was built under President-turned-dictator Gerardo Machado between 1926–1928. The five circular blocks, with cells constructed in tiers around central observation posts, were built with the capacity to house up to 2,500 prisoners in humane conditions.
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After Fidel Castro's revolutionary triumph in 1959, Presidio Modelo was used to jail political dissidents, counter-revolutionaries, homosexuals, Jehovah's Witnesses, and anyone else considered unfit or an enemy to the new norms and dictates of the Socialist Cuban State. By 1961, due to the overcrowded conditions (6,000 to 8,000 political prisoners at one time) it was the site of various riots and hunger strikes, especially just before the Bay of Pigs invasion, when orders were given to line the tunnels underneath the entire prison with several tons of TNT.
Prominent Cuban political prisoners such as Armando Valladares, Roberto Martín Pérez, and Pedro Luis Boitel were held there at one point or another during their respective incarcerations. It was permanently closed by the government in 1967.
The prison now serves as a museum and is declared a National Monument, and the old administration building now serves as a school and research center.