Steven D. Green, a 21-year-old former private first class who was discharged from the army "due to a personality disorder," appeared in a federal magistrate's courtroom in Charlotte, North Carolina, on Monday.
The charges follow a military investigation involving up to five soldiers in the rape and killing of a woman in Mahmoudiya and three of her relatives, one of them a young girl believed to be about 5 years old.
Prosecutors said Green and others entered the home of a family of Iraqi civilians, where he and others raped the woman before Green shot her and her relatives. According to an accompanying affidavit, photos taken by army investigators showed the burned body of "what appears to be a woman with blankets thrown over her upper torso."
Green and three other soldiers were working at a traffic checkpoint in Mahmoudiya, 30km south of Baghdad, on March 12 when the incident took place.
According to an account shown to magistrates, the soldiers changed their clothes before going to the woman's residence to avoid detection. Once there, the affidavit said, Green took three members of the family - an adult male and female, and a girl estimated to be 5 years old - into a bedroom, after which shots were heard from inside.
"Green came to the bedroom door and told everyone, 'I just killed them. All are dead,"' the affidavit said.
The affidavit is based on interviews conducted by the FBI and investigators at Fort Campbell with three unidentified soldiers assigned to Green's platoon. One of the soldiers said he witnessed another soldier and Green rape the woman.
"After the rape, (the soldier) witnessed Green shoot the woman in the head two to three times," the affidavit said.
The case is being handled by federal prosecutors because Green, who served 11 months with the 101st Airborne Division, is no longer in the military.
He faces a possible death sentence if convicted of murder.
On Friday, the US military acknowledged that a criminal investigation had been ordered into the alleged murder of a family in Mahmoudiya.
Four members of the the 101st's 502nd Infantry Regiment have had their weapons taken away and were confined to a US base near Mahmoudiya, officials said.
The suspects belong to the same unit as two soldiers who were kidnapped and killed south of Baghdad last month.