Among the many aspects of the U.S.-Egypt relationship, few have been as controversial as the CIA’s extraordinary rendition program, where the agency frequently handed over suspected terrorists to foreign governments with histories of torture and illegal detention.

According to Human Rights Watch, Egypt welcomed more CIA detainees than any other country from the 1990s through 2005. And while renditions happen only with the assurance that a foreign partner will not torture the prisoner, as one CIA officer once told Congress, the assurances “weren’t worth a bucket of warm spit.” (Want to know more about rendition? Here’s a good backgrounder.)

In the case of Egypt, the assurances were given by Omar Suleiman, former head of the country’s intelligence service, and the man President Hosni Mubarak picked as his vice president a few days ago.

Perhaps the most notorious case is that of Ibn al-Shaikh al-Libi, a Libyan national captured by Pakistani authorities in the months after the September 11, 2001 attacks. According to a 2006 Senate Intelligence Committee report, [PDF] al-Libi was turned over to American authorities and eventually sent to Egypt, where his fabricated testimony, given under torture, became a key piece of “evidence” falsely linking al-Qaeda to Saddam Hussein.

According to the Senate report, al-Libi said he began to feed his captors false intelligence once American interrogators threatened to send him to a foreign government. He started talking, he said, but was sent to Egypt anyway. He later told the CIA that his Egyptian captors placed him in a box less than 2 feet square for 17 hours.

Then, “when he was let out of the box, al-Libi claims that he was given a last opportunity to ‘tell the truth.’ ” He was struck down, he said, and finally “was punched for 15 minutes.” In another episode, he says he was beaten in a way that wouldn’t leave any marks.

As The New Yorker’s Jane Mayer and others have detailed, the “intelligence” he provided made its way into the 2003 speech that Secretary of State Colin Powell gave to the United Nations, laying out the evidence to justify war with Iraq. Years later, after no weapons of mass destruction were found, al-Libi recanted.

“When the F.B.I. later asked him why he had lied, he blamed the brutality of the Egyptian intelligence service,” Mayer writes. “Libi explained, ‘They were killing me,’ and that, ‘I had to tell them something.’ ”

Another famous case is that of Osama Mustafa Hassan Nasr, an Egyptian cleric who disappeared for a year after he was snatched off the streets of Milan in 2003 and taken to Egypt. Known in the agency as “The Italian Job,” the operation was exposed when Italian prosecutors were able to reconstruct the kidnapping after Nasr was released. In 2009, an Italian court convicted 23 Americans in absentia for the kidnapping.

A 2005 report from Human Rights Watch documented 63 cases of people being rendered to and from Egypt, though the report also estimated that the total number of cases was much higher, with as many as 200 people sent away since 2001. The United States was involved in most but not all of those cases, according to the report.

Muhammad al-Zawahiri, the brother of high-ranking al-Qaeda member Ayman, was reportedly kidnapped in the United Arab Emirates in 1999. He was presumed dead for years until the Arab press picked up on his detention.

“For more than five years, the Egyptian government refused to answer a single question about al-Zawahiri’s whereabouts, and allowed his family to believe that he had died rather than disclose his continued incarceration,” the HRW report said. His brother Hussain was also abducted in 1999, reportedly with help of the CIA in Malaysia, according to the report.

Days after taking office, President Obama signed an executive order restricting renditions but also keeping them as an option. "Obviously you need to preserve some tools – you still have to go after the bad guys," an administration official told the Los Angeles Times.

In September, a federal appeals court ruled that detainees cannot sue the CIA over allegations of torture at the hands of foreign governments.