IN THE IMMEDIATE AFTERMATH of the atrocities of September 11, 2001, Islamist influence in U.S. federal and state prisons came under scrutiny from the Justice Department's Bureau of Prisons (BOP). Officials were informed of pre-9/11 complaints by inmates whose Islam (mainly acquired by conversion) was counterposed to a jailhouse infiltration campaign promoting Saudi-financed Wahhabism.

The discontented convicts charged that Wahhabi-trained Muslim chaplains had acquired a monopoly in the correctional system and were busily imposing their ultra-fundamentalist religious interpretation in the vulnerable atmosphere of the prisons. The Wahhabi imams, it was said, had confiscated non-Wahhabi literature from Muslim prisoners, ostracizing and even physically threatening those who contradicted them.

At that time, the prison imams were trained and certified, along with Islamic chaplains in the U.S. military, by two institutions. The first was the former Graduate School of Islamic and Social Sciences (GSISS)--renamed Cordoba University and located in Ashburn, Va., since 2005. The second was the Islamic Society of North America (ISNA), a body mainly supported by radicals from Saudi Arabia and Pakistan. GSISS was raided by U.S. antiterrorism investigators in the GreenQuest inquiry of 2002. ISNA is an unindicted coconspirator in the current court proceeding in Dallas against the Holy Land Foundation for Relief and Development (HLF). The Holy Land Foundation is charged with financing terrorism by serving as a front for Hamas, and was shut down by the federal authorities at the end of 2001.

Right after 9/11, federal prison authorities appeared visibly uncomfortable with the Wahhabi chaplain challenge. The problem brought up constitutional issues, but also exposed the ignorance about Islamic affairs that made much of the American government susceptible to Islamist intrigues, and the difficulty of removing the chaplains from service once they had become government employees.

Yet the prisons produced more and more evidence that something profoundly threatening to domestic security was taking place behind bars. In 2003, then-governor of New York George Pataki dismissed Warith Deen Umar, head of the Muslim chaplains in that state's prisons, for speaking in praise of Osama bin Laden. Umar had planted a network of equally-radical chaplains throughout the state's lockups; but he alone was removed, while the rest remained in place. In the following years other Muslim prison chaplains who had dedicated themselves to hateful and inflammatory rhetoric were exposed, but little action was taken against them (see "Islam in the Big House").

Also in 2003, attention was drawn to a small group of Shia Muslims in the New York prisons who revived an ongoing lawsuit against the Wahhabi chaplains. In 2006, a federal court found merit in the Shia claim of discrimination. Nevertheless, documenting and removing radical Islam from American prisons proved to be no easy task. It was not helpful that anti-radical Muslims who claimed to possess piles of inmate letters complaining about their mistreatment by the Wahhabis never released the material.

Meanwhile, in 2004 the Inspector General of the federal BOP issued a report in which the IG effectively exonerated the BOP for allowing Islamist radicals to seize such sensitive positions inside the correctional system, but suggested a practical measure to at least partly address the problem: "Our fieldwork also revealed that supervision of chapel libraries is not as thorough as it should be. None of the chaplains at the facilities that we visited was able to produce an inventory of the books and videos available to the inmates, and it did not appear that these materials had been evaluated after the terrorist attacks of September 11. We recommend that the BOP undertake an inventory of chapel books and videos to confirm that they are permissible under BOP security policies. The BOP also should consider maintaining a central registry of acceptable material to prevent duplication of effort when reviewing these materials."