Authorities said the baby was found near where his aunt was taken into custody in Iowa after leaving the home in the middle of the night early Thursday.
The baby's 18-year-old mother called 911 after waking about 4:30 a.m. Thursday to find that her son, Kayden Powell, was missing from his bassinette in a room where she was sleeping at a home in the Town of Beloit, authorities said.
Police said Thursday night that about 40 officers from federal, state and local law enforcement agencies were working on the case, but no suspects have been identified and no have been arrests made.
The baby's mother, Brianna Marshall, and the infant's 23-year-old father, Bruce Powell, were staying at the house, Town of Beloit Police Chief Steven Kopp said. Investigators were questioning people who were at the house Wednesday night, Kopp told The Janesville Gazette.
Police said the infant's mother and father continue to be cooperative.
A woman who had been at the house but left around 1:30 a.m. Thursday - the last time people at the residence saw the baby - was questioned but is not a person of interest in the case, the police chief said.
The baby's aunt was visiting the home Wednesday evening but left early Thursday for Colorado where she lives. Police were able to reach the woman on her cellphone, and she pulled off the highway in Iowa. Authorities took Kristin Smith into custody on an unrelated outstanding warrant from Texas at a convenience store along I-80.
Police say they found baby clothes in the aunt's car but not the baby. FBI Agents are on the way to Iowa to question Smith.
The incident is not believed to be a custody dispute, Kopp said. An Amber Alert was not issued because the disappearance doesn't meet the criteria, he said. The FBI and Wisconsin Department of Justice are assisting with the investigation.
Police were still at the house Thursday evening. Authorities kept media away from the small A-frame home. The Town of Beloit, home to about 7,700 people, is about 50 miles south of Madison near the Illinois border.
In cases such as this for authorities, the first few hours are critical. Authorities have searched dumpsters in the area of the home, but say they have found no trace of the 5-day-old baby boy, who's 20 inches long, 6 lbs., and has brown hair and brown eyes.
The Associated Press contributed to this report.