Three Michigan State players -- running back Delton Williams, safety Kenney Lyke and defensive end Gabe Sherrod -- held their right fists in the air while standing for the anthem before the eighth-ranked Spartans' 30-6 loss to No. 11 Wisconsin.
Michigan State coach Mark Dantonio said the players were exercising their freedom.
"To me, your patriotism, your faith are sort of the same -- that's your choice. And it's influenced by what you've experienced in this world. So whether somebody salutes or puts a hand over their heart, everybody has a choice to make," Dantonio said after the game. "I guess they have decisions that people have to make. As long as it's done in a peaceful way, this is America. That's what the flag stands for. It stands for the freedom to do what you need to do. That's the beautiful thing about this country.
"At some point in time, when the true enemy comes, I guess we'll all stand together. But I can't make assumptions for our players, for what they've gone through in their lives. All I can do is try and lead the best way I can and be positive and accepting toward our football team and our players. When we come together after the national anthem, we come together in solidarity, and I think that's what's important."
Later on Saturday, Michigan players held their right fists in the air on their home sideline while the national anthem played at the Big House.
Michigan All-American cornerback Jourdan Lewis was among the Wolverines with their hands in the air. Others included tight end Khalid Hill, outside linebackers Mike McCray and Devin Bush and inside linebacker Elysee Mbem-Bosse. Lewis, who has previously spoken up about social justice issues, said weeks ago that he thought Colin Kaepernick's protest made some important points, but he wasn't sure the best way to voice those concerns.
After the game, Wolverines coach Jim Harbaugh said he backed his players' actions.
"I've been thinking a lot about this over the last four, five, six weeks," Harbaugh said. "Because I am the football coach doesn't mean I can dictate to people what they believe. I support our guys. I think this is something. It's not going away, it's gonna keep happening."
Kaepernick, the San Francisco 49ers quarterback, received national attention when he refused to stand for the anthem before NFL preseason games earlier this year. He cited racial injustice and police brutality among the reasons for his actions.
Since then, other athletes all over the U.S. have engaged in their own protests during the anthem.
Weeks ago, Harbaugh was asked about Kaepernick's anthem protest and said he understood the motivation for them but did not "respect the action."
Harbaugh coached Kaepernick in San Francisco for four seasons before leaving for the Michigan job in late 2014.
In Chapel Hill, North Carolina, on Saturday, about 50 student protesters in the west end zone sat with raised fists during the playing of the anthem before the Tar Heels' game against Pittsburgh.
North Carolina sophomore Jerome Simpson, one of the organizers of the demonstration, said several fans sitting nearby criticized the group for not standing. He said it was not the group's intention to offend.
"We're not anti-police department or anti-military," Simpson said. "The police here in Chapel Hill have been very supportive about making sure this is a welcoming environment. I love that our troops fight for our rights to be able to do this."
Nebraska players Michael Rose-Ivey, Daishon Neal and Mohamed Barry also kneeled before the No. 20 Cornhuskers' game at Northwestern.
ESPN staff writers Dan Murphy, Brian Bennett and David Hale contributed to this report.