One of the men, a citizen of both the U.S. and Jordan, is also accused of threatening to kill or injure President Bush, according to the indictment released Tuesday.
All three had lived in Toledo within the last year and were arrested over the weekend, Assistant U.S. Attorney David Bauer said.
"This case stands as a reminder of the need for continued vigilance in the war on terrorism," Attorney General Alberto Gonzales said at a news conference in Washington.
The man charged with threatening the president, Mohammad Zaki Amawi, 26, pleaded not guilty in Cleveland U.S. District Court. The other two were being arraigned in federal court in Toledo later Tuesday.
The indictment does not specify if any attacks were imminent but says the suspects recruited others as early as November 2004 to train for a violent holy war against the United States and its allies in Iraq.
Two of the men discussed plans to practice setting off explosives on July 4, 2005, so that the bombs would not be noticed, the indictment alleges. It's not clear if the suspects went through with those plans.
The indictment says the group also traveled together to a shooting range to practice shooting guns and studied how to make explosives.
It also alleges that at least one of the men researched and solicited funding for the training, including getting unspecified government grants and private sponsors. The indictment does not say which government or name any potential sponsors.
Amawi is accused of twice threatening in conversations to kill or injure Bush. He also is charged with distributing information about the making and use of an explosive device.
The others are Marwan Othman El-Hindi, 42, a U.S. citizen born in Jordan; and Wassim I. Mazloum, 24, who came to the U.S. from Lebanon in 2000,
Mazloum operated a car business in Toledo with his brother. The indictment accuses him of offering to use his dealership as a cover for traveling to and from Iraq so that he could learn how to build small explosives using household materials.
El-Hindi is accused of trying to get a U.S. citizen with a military background to travel with him in November 2004 to the Middle East as part of the suspects' plan to establish a terrorism training center. The indictment does not identify the military person, referring to him or her throughout the document as "the trainer."
The Department of Justice said the trainer was working on behalf of the government and was cooperating from the beginning of the investigation.
All three men are charged with conspiracy to kill, kidnap, maim, or injure people or damage property in a foreign country, the most serious count that carries a maximum penalty of life in prison if prosecutors prove intent to kill. The three were also charged with conspiracy to kill U.S. nationals, and harboring or concealing terrorists.
Amawi also is charged with unlawfully importing, manufacturing, distributing or storing explosive materials and with making threats against the president.