Israeli authorities say the three abducted, beat and burned Mohammed Abu Khdeir, 16, "only because he was an Arab," the Jerusalem district attorney said. Abu Khdeir's body was found in a Jerusalem forest on the morning of July 2.
Prosecutors allege the killing was retaliation for the deaths of three Israeli teens whose bodies were found in the West Bank in late June.
"The indictment (that was) filed elaborates on a serious and shocking racist act carried out against (an) innocent boy," the attorney general's office said.
The suspects are a 29-year-old man from the West Bank settlement of Adam and two of his 16-year-old relatives -- one from Jerusalem and the other from Beit Shemesh, Israel, prosecutors said.
Abu Khdeir was heading from his home to a mosque in the middle-class neighborhood of Shuafat in East Jerusalem for prayers around 4 a.m. on July 2 when three people forced him into a car and drove off, his father, Hussain Abu Khdeir, told CNN.
Prosecutors say the three defendants strangled and beat Abu Khdeir. Then, while he was unconscious, they burned him to death, prosecutors say.
News of the boy's death led to several clashes in Jerusalem's Palestinian neighborhoods, the biggest of which was centered in Shuafat. Residents there threw stones at security forces, and Israeli authorities responded with occasional volleys of stun grenades and tear gas.
During one of those clashes on July 3, Abu Khdeir's American cousin, Tariq Abu Khdeir, 15, was beaten by Israeli police. Amateur video showed Israeli police officers holding down, punching and kicking Abu Khdeir, a Florida resident who was visiting relatives.
The 15-year-old and his family have said he did nothing wrong, and he returned to Florida this week after a brief home detention. Israeli authorities say they have suspended a police officer accused of beating him.
The death of the Palestinian teen, Abu Khdeir, came less than a month after three Israeli teens -- Eyal Yifrach, 19; Gilad Shaar, 16; and Naftali Frankel, a 16-year-old dual U.S.-Israeli citizen -- were abducted while hitchhiking home from school in the West Bank. They were found dead on June 30.
The Israeli government blamed the Islamic militant group Hamas, which praised the abductions but denied it was responsible.
Israel responded in part by arresting Hamas activists. Militants in Gaza, the Palestinian territory that Hamas controls, stepped up rocket fire into Israel, and Israel responded with airstrikes.
Starting roughly on July 7, Israel started an intense anti-Hamas airstrike operation in Gaza. At least 230 Palestinians have been killed and close to 1,700 have been injured since the operation began, according to Palestinian health officials. The rocket fire from Gaza has killed one man in Israel.
Defendants accused of other crimes against Arabs
Two people indicted in Abu Khdeir's death -- the man and one of the minors -- also are accused of trying to commit crimes against Arabs in the East Jerusalem area on July 1, including trying to kidnap a 7-year-old and trying to burn cars, the Jerusalem attorney general's office said. As in the Abu Khdeir case, revenge was the motive, prosecutors said.
They hurt both the child and his mother, prosecutors alleged without elaborating.
Earlier, on June 15, the same two burned a shop in the Palestinian village of Hizma near Jerusalem because the man was angry with someone there, prosecutors said.