Rallying supporters on social media with the hashtag #SanctuaryCampus, organizers said actions were planned at more than 80 schools, including Vermont's Middlebury College, where about 400 people gathered, and Yale University, where demonstrators numbered about 600.
Students sought assurances that their schools would not share their personal information with immigration officials or allow Immigration and Customs Enforcement agents on campus.
"Can you imagine the fear that it would inflict on college campuses if having ICE agents walk into a campus becomes the status quo?" organizer Carlos Rojas of the group Movimiento Cosecha, said by phone from New Jersey. "It would be terrifying."
"I'm very fearful," Miriam Zamudio, whose parents brought her to the US from Mexico as a child, said by phone as she prepared to join a protest at Rutgers University in New Jersey.
She worries that the family information she provided on her application for Deferred Action for Childhood Arrivals status will endanger her parents, who are living in the country without legal permission.
Several hundred people, mainly high school and college students, rallied at the federal building in downtown San Diego to protest Trump's election. Some held signs or banners saying "we are not criminals" and "make racists afraid again."
An 18-year-old was arrested after he allegedly punched a police officer, police said.
In one non-campus protest on Wednesday night, hundreds of people rallied on the steps of Los Angeles City Hall to protest Trump's appointment of Steve Bannon as a senior adviser.
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