The league had already faced public relations problems after other high-profile players were found to have C.T.E., including Junior Seau, Ken Stabler and Frank Gifford. Mr. Seau — along with Dave Duerson, Andre Waters and Ray Easterling, among others — killed himself.
For years, Mr. Hernandez was held up as a particularly egregious example of N.F.L. players running amok off the field.
Just 10 months after he signed a $40 million contract with the Patriots in 2013, with the promise of becoming a superstar, the body of a friend who had been shot multiple times was discovered. Mr. Hernandez was convicted of the friend’s murder, and later accused in two other killings from 2012. Just days after an acquittal in that case, he hanged himself with a bedsheet in his prison cell.
The researchers did not make a direct link between Mr. Hernandez’s violence and his disease.
But C.T.E. is often marked by problems with controlling aggression and impulses, and some degree of dementia, as well as mood swings, lapses in judgment and a disorganized manner.
Mr. Hernandez’s estate filed a federal lawsuit on Thursday against the N.F.L. and the Patriots seeking damages to compensate his 4-year-old daughter for the loss of her father. The suit alleges that the league and the team knew that repeated head hits could lead to brain disease, yet did not do enough to protect Mr. Hernandez from those hits.
The lawyer, Jose Baez, said the family was also contemplating suing the N.C.A.A. and the University of Florida, where Mr. Hernandez played before playing for the Patriots.
The N.F.L. did not comment on the medical finding, and it declined to comment on the suit. The Patriots declined to comment. Soon after his arrest in 2013, the team distanced itself from him, buying back more than 1,200 Hernandez jerseys from fans.
The trauma to Mr. Hernandez’s brain raises fresh questions about the dangers of playing tackle football. This week, other researchers at Boston University published research that found that adults who began playing tackle football before they were 12 years old developed more cognitive and behavioral problems later in life than those players who started tackle football after they reached that age.
The fact that Mr. Hernandez also led a troubled life off the field will complicate the N.F.L.’s efforts to calm jitters about the sport because it will probably make some people wonder whether football had a role in his violence away from the game.
Mr. Baez said that in hindsight, Mr. Hernandez’s family had witnessed him act in ways that were consistent with a person found to have C.T.E., “but you don’t know.”
The slides of Mr. Hernandez’s brain samples were unambiguous and graphic.
Dr. Ann McKee, chief of neuropathology at the VA Boston Healthcare System and director of the CTE Center at Boston University, examined his brain and said in a statement that Mr. Hernandez had “early brain atrophy” and “large perforations in the septum pellucidum, a central membrane” of the brain. The slides also showed what she called “classic features of C.T.E. in the brain,” including deposits of tau protein in the front lobes of the brain in nerve cells around small blood vessels.
The discovery of C.T.E. adds another turn in Mr. Hernandez’s meteoric rise and fall. After a standout career at Florida, he was signed by the Patriots in 2010. Just years before, he had been working menial jobs in Bristol, Conn., his hardscrabble hometown, where he drove a $300 used car he bought with money borrowed from friends.
At Florida, he helped the Gators win the national title in the 2008 season. But he fell to the fourth round of the N.F.L. draft because of off-field issues including involvement in a bar fight.
Less than a year after he signed the contract with the Patriots that might have provided a stable future, his friend was found murdered. His conviction in the case became a stark example of N.F.L. players who exhibit violence off the field.
Even his demise was filled with turmoil. After Mr. Hernandez died, Mr. Baez called a news conference in front of the Office of the Chief Medical Examiner and accused the state of illegally withholding Mr. Hernandez’s brain. Mr. Hernandez’s body had been discovered the day before, tied with a bedsheet to the window of his prison cell in Shirley, Mass. His death was later ruled a suicide.