Edgar Ray Killen, 80, was taken to hospital to be treated for high blood pressure just before testimony was heard from relatives of the victims, Michael Schwerner, James Chaney and Andrew Goodman.
The three men were killed when promoting black voting rights in the "freedom summer" of 1964, in a case that helped galvanise the civil rights movement, and inspired the 1988 film Mississippi Burning.
The defendant, a part-time preacher and sawmill worker, was taken ill after the judge ruled that evidence from a 1967 federal trial, including the evidence of long-dead witnesses, was admissible.
His condition was stable, but the trial went into recess until today at the earliest, depending on his ability to attend.
The judge's decision to admit earlier evidence could prove significant. After local authorities failed to bring any of the murder suspects to trial, the justice department in Washington tried them three years after the murders, on the federal charge of "violating the civil rights" of the victims.
Seven white men were jailed in that trial, but Mr Killen walked free after the jury could not come to a unanimous verdict. One juror later said she could not convict a preacher.
In opening statements, Mr Killen's lawyers admitted that he was a member of the Klan in Mississippi's Neshoba county, where the killings took place. But they said he was merely a messenger who passed on a decision to kill the three rights activists by the Klan's "imperial wizard", Sam Bowers.
The three victims - Mr Chaney, a black man from Mississippi, and Mr Schwerner and Mr Goodman, white men from New York - were picked up by the local police when they visited the ruins of a black church burned down in June 1964.
The police released them in the middle of the night. They were then hunted down, shot and buried in an earth dam.
Mitch Moran, a defence lawyer, said: "Edgar Ray Killen was just a bystander in an organisation a lot of other people were in ... The Klan is not on trial in this case."
He added: "As repulsive as an organisation like that might be, you can't find him guilty for the crime he's charged with."
Mr Moran admitted that Mr Killen was the klansman, previously unidentified, who had reportedly told one of the 1967 trial defendants: "We have a dozer and a place to bury them."
However, that statement, Mr Moran argued, only proved his client had knowledge of the crime - not that he had a direct role in it.
The defence argues that only a person who pulled the trigger can be found guilty. Legal experts say that is not necessarily true under Mississippi law.
Earlier, the state's attorney general, Jim Hood, said prosecutors intended to prove that Mr Killen planned the murders and helped round up klansmen to chase down the trio. Testimony will also show that Mr Killen used the pulpit to encourage church members to join the Klan, said Mr Hood
Mr Killen's name has been associated with the murders from the outset. FBI records and witnesses indicate that he organised the carloads of men who chased the victims. He could get life in prison if convicted.