Osama Mustafa Hassan was seized by the CIA and flown to Egypt, where he says he was tortured.
Seven Italians were also indicted, including Italy’s ex-military intelligence chief, Nicolo Pollari.
The case would be the first criminal trial over the secret US practice known as “extraordinary rendition”.
During rendition, people suspected of involvement in terror activities are taken from one country and flown to another, where many claim they are tortured.
Most of the indicted US citizens are believed to have returned home from Italy.
The Italian government has yet to decide whether or not it wishes to request their extradition.
Prime Minister Romano Prodi is coming under renewed pressure to do so at a time when Italian-US relations are sticky at best, says the BBC’s Christian Fraser in Rome.
The US has never commented on the case.
Those indicted include the former station chief of CIA operations in Milan, Robert Seldon Lady, who says his opposition to the proposal to kidnap the imam was over-ruled.
He is reported to be among those who have returned to the US, leaving behind a villa in Italy which he bought with his life savings.
Mr Pollari, the former head of the Italian secret service, SISMI, had already been removed from his job following a parliamentary inquiry into the claims.
Of the seven Italians who were charged, six were charged with abduction and one is accused of withholding information on abductions.
Lawyers say they have compiled thousands of pages of documents and testimony from Italian agents past and present, some of whom have acknowledged working with the US in planning the abduction.
The trial is due to begin on 8 June.
Mr Hassan, also known as Abu Omar, was released from prison in Egypt only on Sunday.
He says that he was repeatedly beaten and tortured during his four years of detention in Cairo.
He described one form of torture in which he was forced to lie on a wet mattress through which an electric current was passed.
Mr Hassan still faces the risk of arrest as a terror suspect if he returns to Italy, our correspondent says, but his lawyer has said that he wishes to come to Milan nonetheless to testify during the trial.
On Wednesday, EU lawmakers endorsed a damning report accusing some member states of turning a blind eye to rendition, naming Italy as one of the countries involved.