Jimmy Lee Dykes, 65, was holed up in a bunker in the southeastern Alabama community of Midland City with the boy for nearly a week.
The standoff ended Monday when special FBI teams stormed the bunker, rescued the boy, and killed Dykes in a firefight.
Dale County Coroner Woodrow Hilboldt pronounced Dykes dead at 8:58 p.m. Wednesday after the property, which was initially rigged with explosives, was deemed safe by the FBI.
The coroner declined to say how many times Dykes had been shot or where the wounds were on his body but did confirm he had died of multiple gunshot wounds.
Hilboldt said the body was taken to a state forensics laboratory in Montgomery for an autopsy.
FBI Special Agent Paul Bresson said a shooting review team from Washington was also reviewing the hostage-taking episode, which began Jan. 29 and ended Monday.
The 5-year-old boy celebrated his sixth birthday Wednesday and is said to be doing well despite the hostile ordeal.
The Associated Press contributed to this report.
