Investigators say the second child is expected to survive after suffering blows by his foster father.
No one can say how long the brothers were in this family's care. One of them is now in a Milwaukee hospital, the other is dead.
"It's a tragedy for all involved," Dave Titus with Dodge County Human Services says.
Investigators say the tragedy started at a home in Waupun, a foster home to a couple of young brothers.
"More than likely, the foster home license will be canceled at some point," Titus says.
The suspect, Shane Marquardt, now resides at the Dodge County Jail. He appeared in court by video conference before a tearful crowd, including his wife. The 31-year-old house designer faces charges of first degree reckless homicide and first degree reckless injury.
"He stated he just lost it, lost his temper because, I believe, one of the children vomited in his bed," Dodge County District Attorney Steve Bauer says.
The criminal complaint against Marquardt says the suspect woke up the two boys around eleven o'clock Friday morning, then noticed the three-year-old had thrown up in his bed.
"The defendant here struck the one child two to three times as hard as he could with his fist into the abdomen of the child," Bauer says.
Then, according to the complaint, Marquardt also struck the younger brother, as he would punch the punching bag in his basement.
"He stated that he then put the children to bed and later [the three-year-old] started vomiting which ultimately caused him to call EMS," the complaint states.
An autopsy shows the three-year-old suffered severe internal injuries.
"This is a criminal case. There are allegations ... have to prove them. Based on evidence, I'm confident we'll be able to do that," Bauer says.
Meantime, Titus says an internal investigation is underway. But he defends the system designed to protect children in need.
"Someone asked me how did this fall through the cracks. It really isn't a fall through the cracks issue. There was criminal behavior. It happened. The individual responsible will be dealt with," Titus says.
Marquardt has no prior criminal record. The judge set bail at $60,000. Marquardt is due back in court on May 18.