Wilfredo Elias, 29, could face life in prison if convicted in the case.
Prosecutors say he was arrested in Missouri last week while traveling with a carnival.
An electronic memory storage device containing videos of the incidents was recovered by authorities, according to the Office of Cook County State's Attorney Anita Alvarez.
Elias could face natural life in prison if convicted.
Elias was extradited to Chicago where he was ordered held without bond. A preliminary hearing in his cases is scheduled for Oct. 5.
According to prosecutors, last July a witness discovered a USB computer memory storage device in a family storage area that belonged to Elias. When he plugged it into his computer, the witness said that the device contained multiple video files with one of those files depicting the defendant sexually assaulting a child.
Task force investigators recovered multiple video images showing Elias assaulting both the victim, who was determined to be 3 years old, and another 2-year-old girl. Investigators were able to identify both victims and learned that they had both been left in the care of the defendant at various points over the last year.