The Gotham State Penitentiary was the primary correctional facility of Gotham City prior to the establishment of Blackgate Island. It is located in the neighborhood of Sommerset, some twelve miles north of Arkham Asylum. Although Gotham's more deranged criminals were usually incarcerated at Arkham, the Gotham State pen filled its cells with prisoners who were just as notorious, but no less deadly such as the Penguin, Catman, Deadshot, and the Cavalier.
On one occasion, the penitentiary fell into the hands of a mob boss and Batman infiltrated into the penitantiary, with help from Commissioner Gordon, to investigate this organized crime racket working from inside. With help from Robin, they managed to break the organization and returned the control of the prison to the authorities.
After a violent riot, the inmates took control of the penitentiary. They demanded that Commissioner Gordon would come to deal with them. This proved to be a bad choice for the criminals, as Gordon managed to restore order and regain control of the prison single-handedly.
Shortly after the Crisis on Infinite Earths event, the Gotham State Pen was the scene of a massive breakout executed by the eco-terrorist Ra's al Ghul. Ra's not only released all of the prisoners from the prison, but he also provided them with their costumes and weapons, while simultaneously uniting them with escaped patients from Arkham Asylum. 
- Warden Michael Pendergast (Staff)(formerly)
- Warden Brewster (Staff)(formerly)
- Warden Rothstein (Staff)(formerly)