He was charged with molesting seven girls, many of whom are gymnasts, while working for USA Gymnastics and Michigan State University.
As part of the plea deal, Nassar, 54, could face at least 25 years in prison.
The hearing comes after a third former US Olympian, Gabby Douglas, accused him of sexual abuse.
Douglas reveals abuse by team doctor
In a statement to the court on Wednesday, Nassar said he was pleading guilty to "move the community forward and stop the hurting".
"I'm so sorry that this was like a match that turned into a forest fire, out of control," he said.
"I want them to heal. I want this community to heal. I have no animosity toward any one. I just want healing. It's time."
"You used that position of trust that you had in the most vile way - to abuse children," Ingham County Court Judge Rosemarie Aquilina said, noting that sex abuse is a nationwide "epidemic".
"You violated the oath that you took, which is to do no harm, and you harmed them. Selfishly."
Many of his accusers testified that they were abused while he was examining the young athletes, and sometimes while their parents were nearby.
He has been accused of abusing more than 130 women - including Olympic gold medalists Ms Douglas, Aly Raisman and McKayla Maroney - during his time as team doctor for the US women's gymnastics team.
Ms Douglas, who was one of the so-called Fierce Five that won gold medals at the London Olympics in 2012, revealed her accusation on Instagram.
"I didn't publicly share my experiences as well as many other things because for years we were conditioned to stay silent and some things were extremely painful," she wrote.
During the hearing Ms Raisman, a member of the 2012 and 2016 Olympic teams, tweeted that she was "disgusted" that Nassar, who lost his licence, was referred to as a doctor.
Nassar's case was part of a scandal which saw USA Gymnastics president Steve Penny resign last year. Mr Penny was accused by victims of failing to quickly notify authorities about abuse allegations.
In a statement after the plea deal was announced, USA Gymnastics - the organisation which determines the US Olympic team - said it is "very sorry that any athlete was harmed" by their former doctor.
They added that it was "important" that he acknowledged "his appalling and devious conduct" in court and said the deal "permits punishment without further victimisation of survivors".
Nassar has already pleaded guilty to multiple charges of child pornography in federal court and could face a maximum sentence of life in prison.
Before accepting the plea, Judge Aquilina asked him to confirm that he did not wear gloves when abusing his victims between 1998 and 2015, when he was fired.
The alleged examinations were "not for any medical purposes is that right? It was for your own purpose, is that right?", the judge asked. Nassar responded: "Yes."
He is due to be sentenced on 12 January.
[BBC SOURCES]
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