Oceanside Police Chief Frank McCoy told reporters outside Seau's home the former San Diego Chargers linebacker had been discovered in a bedroom by a woman identified as his girlfriend.
Police told the Los Angeles Times no suicide note was found and that no foul play was suspected.
Seau, 43, played 17 years in the NFL and made the Pro Bowl a dozen times. He was drafted by the Chargers in 1990 out of the University of Southern California and played in San Diego through 2003. He finished out his career with New England and Miami before retiring in 2009.
"Everyone at the Chargers is in complete shock and disbelief right now," the Chargers said in a written statement. "We ask everyone to stop what they're doing and send their prayers to Junior and his family."
Seau grew up in Oceanside and his family was on the scene within a few hours of his death. His sister, Annette, asked for privacy but Seau's distraught mother addressed reporters and onlookers, saying she had no indication anything was wrong with her son when the spoke recently.
"I don't understand and I don't know anything about what happened," Seau's mother said. "I appreciate everyone who came out to show your love to my son."
"I pray to God to take me and not my son," she added. "But it's too late."
Seau operated a San Diego restaurant after his retirement as well as an education foundation that assisted children in the San Diego area. KNSD-TV said a check of court records did not indicate any pressing financial issues.
Seau's domestic life attracted the attention of the media and law enforcement in 2010. Seau spent a night in jail after being arrested for domestic violence against a girlfriend. Although no formal charges were filed, Seau drove his car off a cliff in nearby Carlsbad the morning of his release. Seau said at the time he had fallen asleep at the wheel and was not seriously hurt.