"We just found with the Caylee Anthony case how difficult is to get a conviction in a U.S. court," McConnell, R-Ky., told "Fox News Sunday."
Casey Anthony, 25, of Orlando, Fla., was acquitted in the 2008 death of her 2-year-old daughter Caylee. She was sentenced to four years for lying to police -- but because of time served, she will be released from Orange County (Fla.) Jail this week, court officials said.
Suspected terrorists such as Khalid Shaikh Mohammed -- the self-described mastermind of the Sept. 11, 2001, attacks who is scheduled to be tried along with four other suspects in a civilian federal court in New York -- "are not American citizens," McConnell said.
"I don't think a foreigner is entitled to all the protections of the Bill of Rights," McConnell said. "They should not be in U.S. courts. They should be at Guantanamo [Cuba] and before military commissions."
McConnell and other Republicans expressed anger last week after the Obama administration said it would prosecute in civilian court Somali terror suspect Ahmed Warsame, accused of ties to two Islamist militant groups.
Warsame was charged in U.S. District Court in New York with nine counts related to accusations he provided support to the Shabaab Islamist insurgent group fighting to overthrow the government of Somalia and al-Qaida in Yemen.