The victim was identified Sunday as 48-year-old Adan Fabian Perez, a Guatemala native, according to Jo-Ann Farmer, chief deputy coroner for Jefferson County.
Farmer said he was identified by his 19-year-old son, who also works at the track.
"There's a suspicion of foul play," Farmer said Sunday evening. An autopsy is scheduled for Monday.
Louisville Metro Police say the death is being investigated as a homicide, but that there appears to be no connection to the track.
"At this point we don't have anything pointing to the fact that this had any association with Churchill Downs or the Derby itself," said Alicia Smiley, spokeswoman for Louisville Metro Police. "We are still investigating at the stables and at the barn."
Smiley said that the victim "did sustain injuries that lead us to believe he was involved in some type of altercation."
"Our investigation is ongoing as to why he would have specifically been at this location," Smiley said.
Farmer said that the victim resided at the track's worker quarters, but at a different location than where he was found.
Churchill Downs security called police at 4:50 a.m. EDT, Smiley said. The body was found in a barn used by Louisville trainer Angel Montano Sr.
Montano did not have a horse running Saturday either in the undercard or the Derby, which saw a record attendance of more than 165,000. A telephone call, text and Twitter message left for Montano were not immediately returned.
About 200 people live at Churchill Downs at any given time - either in dormitories on the edge of the property or in small apartments above some of the barns themselves.
Although Montano's barn is just four away - about 150 yards - from where this year's Derby winner I'll Have Another is kept, there was little talk of the incident in the stable area.
Instead, I'll Have Another's trainer and owners were participating in the usual post-Derby media interviews and speculating about the next race in racing's Triple Crown, the Preakness Stakes, in three weeks.
The body was removed by stretcher from the barn at 9:50 a.m., and police were seen packing about a dozen large paper bags into the back of a crime scene unit van.
About a week after last year's Kentucky Derby, jockey Michael Baze's body was found in a vehicle near the stables at the famed Louisville track. His death was ruled an accidental drug overdose.
Associated Press writer Norman Gomlak in Atlanta contributed to this report.