The indictment includes two counts of felony murder.
It comes hours after the medical examiner officially ruled the death of Kletzky a homicide, saying he was drugged and smothered.
The autopsy found that Kletzky suffered intoxication by the combined effects of cyclobenzaprine (muscle relaxant), quetiapine (antipsychotic), hydrocodone (pain medication), and acetaminophen (Tylenol) followed by smothering.
Aron was arrested a week ago, accused of kidnapping, killing and dismembering Leiby Kletzky.
He got lost on his walk home from day camp on July 11 and asked a man, Levi Aron, for help, police said.
Brooklyn District Attorney Charles Hynes said evidence shows that Aron took Kletzky to a wedding in upstate New York on the night of his abduction. He apparently sat in the car outside while Aron attended the festivities.
"Detectives now have reason to believe beyond Aron's confession that Leiby was at the wedding, but not necessarily inside the venue," Browne said Wednesday.
A gas station attendant along the route saw the boy go to the bathroom, prosecutors said.
Detectives later found the boy's severed feet, wrapped in plastic, in Aron's freezer, as well as a cutting board and three bloody carving knives. The rest of the boy's body was discovered in bags inside a red suitcase in a trash bin.
Aron has pleaded not guilty to murder and kidnapping charges.
Aron's attorney, Pierre Bazile, had no comment Wednesday on the medical examiner's findings. Bazile has said his client told him he heard voices and suffered from hallucinations. Aron was placed on suicide watch. Bazile said he worried about his mental state - and also said Aron's family was distraught.
Hynes said the investigation continued into whether Aron was suspected of kidnapping or having inappropriate contact with any other children.
For information on a fund set up by the Kletzky family please visit www.leibykletzkymemorialfund.com.
Donations can also be sent to:
NACHMAN & ESTY KLETZKY
C/O RABBI BINYOMIN EISENBERGER
BROOKLYN, N.Y. 11219
(Some information from the Associated Press)