Hastert, 74, entered the Federal Medical Center in Rochester, Minnesota. He is not facing sexual abuse charges because the statutes of limitation have expired. But he pleaded guilty to hiding money transactions, admitting that he paid $3.5 million to keep one victim quiet.
The incidents allegedly happened when he was a teacher and wrestling coach in Illinois in the 1960s and '70s.
Hastert also acknowledged misleading the FBI last year when the agency was investigating the claims.
Judge Thomas Durkin called Hastert "a serial child molester" when he handed down the sentence in April, CNN affiliate WGN reported.
In addition to his prison term, the former Republican lawmaker was ordered to pay $250,000 to a victims' fund and enter a sex offender treatment program.
Some former members of Congress wrote letters to the court asking for leniency and noting Hastert's deteriorating health and "integrity." In recent years, Hastert had two back surgeries, a stroke and sepsis.
"He is a good man that loves the Lord," former House Majority Leader Tom DeLay wrote. "He gets his integrity and values from Him. He doesn't deserve what he is going through. I ask that you consider the man that is before you and give him leniency where you can."
But Scott Cross, who said he was abused by Hastert when he was a teen, said Hastert's actions scarred him.
"As a 17-year-old boy I was devastated," Cross said. "I tried to figure out why Coach Hastert had singled me out. I felt terribly alone. Today I understand I did nothing to bring this on, but at age 17, I could not understand what happened or why."