The NIH findings contribute to a national debate over the long-term health effects of sports concussions.
About 2,000 former players sued the National Football League (NFL) last year, arguing that the league downplayed the risks associated with repeated head injuries.
The league, in turn, has contributed $30 million for related research at the NIH.
And this week, the U.S. Institute of Medicine launched a major study of the issue as it affects young people.
The NIH autopsy of Seau's brain came at the request of his family.
"I don't think any of us were aware of the side effects that could be going on with head trauma until he passed away. We didn't know his behavior was from head trauma," Seau's son, Tyler, told The Associated Press.
Seau retired in 2009 after playing as a linebacker for 20 NFL seasons, many for San Diego.