The three connected to the bombings and a fourth IL man were arrested on Tuesday morning and charged with possession of a machine gun.
It identifies them as Michael B. Hari, 47; Joe Morris, 22; Michael McWhorter, 29.
Bloomington police said the bomb only damaged the imam's office at the center and worshippers extinguished the blaze before firefighters arrived.
A second informant came forward and proved information on Hari, McWhorter and Morris, saying they responsible for the bombing in Bloomington, Minnesota.
According to a statement by the US attorney's office in Springfield, on Tuesday morning, Federal Bureau of Investigation agents arrested four rural east central IL men on charges of possession of a machine gun. All are from Clarence, Illinois, a rural community 35 miles north of Champaign-Urbana.
Hari was arrested Tuesday morning while traveling to a court appearance in Ford County, for a hearing in an assault case.
McWhorter claimed it was Hari's idea to target a mosque, with the intention to "scare them out of the country".
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McWhorter allegedly admitted his involvement in bombing the mosque and the attempt on the women's clinic, and told investigators that each of the three men had specific roles in the attack.
According to a 16-page probable cause statement filed in U.S. District Court in Urbana, the Bureau of Alcohol, Tobacco, Firearms and Explosives received a tip February 19 about potential bomb-making materials at the home of Hari's parents in Clarence.
In announcing the charges against the men, interim U.S. Attorney Gregory Brooker described the bombing as a "tragedy for all Minnesotans".
"While there are still many questions to be asked, we are grateful the people responsible for this attack will be brought to justice", said Jaylani Hussein, the executive director of the Minnesota chapter of the Council on American-Islamic Relations.
Hussein tells The Associated Press that Muslims are glad that the suspects are "no longer a threat to our community".
The Islamic Center primarily serves Somalis in the Minneapolis area and houses a mosque and religious school for children.
Soon after the explosive device was thrown in, the mosque's executive director, Mohamed Omar, said, a member of the congregation rushed outside and saw a truck driving away from the mosque's parking lot. The FBI had offered a $30,000 reward for information leading to a conviction in the bombing. Mosque leaders later released security video from inside the mosque that caught the moments before the explosion, and some smoke and flying debris.