The 29-year-old is accused of having assaulted a total of 70 patients, including 18 adults, while working in several hospitals and health facilities in Sweden.
Prosecutors claim the doctor, who has been held in custody since December 2017, had examined child patients' genitals in cases when it was "medically irrelevant".
The children were aged between two and 12. In four of the cases, "the crime should be deemed aggravated by (the doctor's) recklessness against the child's young age and abuse of his position", prosecutors said in the charge sheet.
The man, who denies the charges, is also accused of filming some of the assaults, and of possessing child pornography.
The doctor, who also worked for an online health care service allowing clients to consult him via video chats, had allegedly asked parents to show their children's genitals.
"The abuse of the trust generally enjoyed by doctors, and the use of a new technology to commit sexual abuse, is unique and worrying," Fredric Wikman, a lawyer representing several victims, told TT news agency.
The doctor, whose trial starts on September 20th, faces up to 14 years in prison if convicted.