At least one of the raids possibly involves a Christian militia group.
Besides Indiana, the FBI targeted properties in Michigan and Ohio. Several arrests were made.
The names of the suspects and exact charges had not been made public Sunday night.
The FBI, Homeland Security and state and local police all descended on a Hammond, Ind. home Saturday night. They blocked off the street and spent three hours searching a brick two-flat building.
Next door at Gusto's Pizza, no one had any idea what was happening.
"I was scared. I was like, 'What did we do wrong?' Until I saw all of them and they started yelling at me to get back inside. I ran back inside, all these swat members and snipers around the house," said George Ponce, who witnessed the raid.
"A half-hour later, an FBI agent apologized, explained what was going on and said they were looking for bombs, homemade bombs," witness Ron Jakuczak said.
While neighbors could not identify any homemade bombs, they say they did see FBI agents haul out boxes of evidence, including guns.
"After they searched the house, they came out with boxes and at least 40 guns," Ponce said.
Over the weekend, the FBI made similar sweeps in two dozen jurisdictions all over the Midwest, including a property in Adrian, Michigan. It is being reported that suspected members of a militia live at the home that was the focus of the raid.
Michael Lackomar, of the southwest Michigan Volunteer Militia, says his group was not the target. He reportedly is told a religious militia group claims their property was raided.
"If they were involved with what went down last night, it would have to be for issues such as unlawful weaponry or maybe something they posted somewhere that they shouldn't have," Lackomar said in a telephone interview.
Overall, the FBI arrested at least seven people. The man they were looking for in the Hammond property was not home. Federal agents caught up with him Sunday morning in Clarendon Hills.
Neighbors say, two brothers lived in the northwest Indiana house. One, they say, owned several German Shepherds and always wore fatigues.
"A couple years ago, he had a personal transport vehicle parked in his yard. We found that very strange, but sometimes people collect. You don't know," one neighbor said.
The person who lives in Hammond was in the custody of the U.S. Marshall in Indiana Sunday night. The FBI would not say whether he is part of a religious militia.
All arrests that were made over the weekend remained under seal.
Some charges were likely to be unsealed Monday, when some of the suspects were expected to appear in federal court.