A prison is a government-run facility where inmates are forcibly confined.
- Ravencroft Institute for the Criminally Insane: A prison for those not mentally fit for regular prisons. Located near New York City.
- Ryker's Island. Handles normal prisons. Located near New York City in the East River between Queens and the Bronx.
- S.H.I.E.L.D. Helicarrier: The floating headquarters for S.H.I.E.L.D. has a prison facility for criminals they don't want the world to know about.
- Vault: A prison for enhanced supervillains.
Puppet Master tried to use the inmates of a prison to take over the world.
John Hardesky was held in the S.H.I.E.L.D. helicarrier's prison facility.
It is possible, though unspecified, that the prison seen in the Fantastic Four episodes "The Origin of the Fantastic Four, Part One" and "The Origin of the Fantastic Four, Part Two" are Ryker's Island.