The indictment was filed in federal court in Detroit.
Weiss was fired in 2023 as Michigan's co-offensive coordinator after failing to cooperate with the school's investigation of his access to computers.
Phone and email messages seeking comment from his attorney, Doug Mullkoff, were not immediately returned Thursday.
From 2015 to 2023, Weiss gained access to the databases of more than 100 colleges and universities that were maintained by a third-party vendor, Keffer Development Services, and then downloaded personal information and medical data of more than 150,000 athletes, the indictment states.
The 14-page document portrays him as a computer whiz, saying Weiss “cracked the encryption protecting the passwords, assisted by research that he did on the internet.”
He then got access to the social media, email and cloud storage accounts of more than 2,000 athletes as well as more than 1,300 students or alumni from schools across the country, according to the indictment.
“Weiss primarily targeted female college athletes,” the indictment said. “He researched and targeted these women based on their school affiliation, athletic history and physical characteristics. His goal was to obtain private photographs and videos never intended to be shared beyond intimate partners.”
Weiss kept notes on photos and videos that he downloaded, commenting on the bodies and sexual preferences and sometimes returning years later to look for new images, the indictment said.
“Our office will move aggressively to prosecute computer hacking to protect the private accounts of our citizens,” Julie Beck, the acting U.S. attorney in Detroit, said of the charges.
After more than a decade as an assistant coach with the Ravens, under coach John Harbaugh, Weiss moved to Michigan to work for Harbaugh’s brother, Jim Harbaugh.
It has been publicly known for two years that Weiss was under scrutiny. His Ann Arbor home was searched by police in January 2023, shortly before he was fired. He said at the time that he was cooperating and was looking “forward to the matter being resolved.”
Weiss' initial court appearance on the charges was not determined.