Cairo’s military courthouse is a nine-story slab of white concrete that rises just off the main road in the Nasr City district, a sprawling zone of condominiums and government buildings designed in part by President Gamal Abdel Nasser following Egypt’s 1952 coup. On a recent afternoon, two armored personnel carriers, guarded by military policemen with red berets, were parked in front of the building, known to Egyptians by the name “C-28.” The MPs were keeping an eye on a small group of protesters who were milling around the entrance gate. While I talked with two lawyers in the heat, a slim young man tried to hurdle over a turnstile at the entrance and unleashed a string of obscenities when MPs pushed him back. A heavyset woman in a black abaya joined in the name-calling, and a melee erupted, with civilians and soldiers screaming at each other and others trying to restrain them. Eventually, the man and the woman were dragged off by their friends and relatives.

Such displays of emotion are not uncommon at C-28 these days. Since February 11, when President Hosni Mubarak ceded power to the Supreme Council of the Armed Forces, between seven and ten thousand civilians have been brought before closed military tribunals inside this fortresslike building. The civilian courts that normally would have tried them were not functioning in the first weeks after the revolution, but now, according to human rights officials, that’s no longer the case. Those arrested have been charged with a variety of offenses, including “thuggery,” assault, and threatening the security of the Egyptian state—a catch-all phrase once employed by Mubarak’s despised ancien regime.

Those accused include pro-democracy demonstrators, bloggers, and other prominent activists swept up in the chaos that preceded and followed Mubarak’s fall, as well as common criminals and bystanders. Thousands have been convicted and sentenced to terms of between several months and five years in prison. The procedures tend to be swift and are conducted before single judges in military uniform who are not known for scrupulous attention to the evidence. In late June, Amnesty International said that trying civilians in military courts violates “fundamental requirements of due process and fair trials.”

According to the military leadership, the tribunals are necessary because of the collapse of the State Security police and the disarray of the state prosecutor’s office. Major General Hassan al-Roueini, the member of the Supreme Council who is responsible for confirming verdicts, has pledged that the tribunals will be phased out as the prosecutor’s office gets up to speed. “I’d…