Polk County Sheriff Pete Johnson said searchers looked into and around the car for Isaiah Theis of Centuria, but didn't open the trunk because they were advised it was locked before the toddler was reported missing Tuesday, the St. Paul Pioneer Press reported.
Wednesday night, however, the owner of the car arrived to move it. When a sheriff's deputy opened the trunk before the owner took off, the boy's body was found.
"The death of an otherwise healthy 2-year-old boy requires a complete and thorough investigation as to any possible cause, whether that cause is accidental or criminal," Johnson said in a release. "At this very early stage of the investigation, the cause and manner of death is unknown."
Johnson said the Wisconsin Justice Department, the Polk County sheriff's office and medical examiner's offices combed the area.
Johnson said a full autopsy would be conducted, adding "it would be inappropriate for anyone to speculate as to the cause and nature of death until that examination has been done.