The four, who included a cleric, were killed on June 23 last year when a hostile mob attacked a house where they had gathered in the village of Abu Mussalam in Giza province.
The charges include the murders of the four men, the attempted murders of 13 others, vandalism and arson. The trial is due to open on December 21.
The killings came the month before the army ousted elected Islamist president Mohamed Morsi and followed weeks of toxic anti-Shiite rhetoric in the Egyptian media and from Sunni Islamist leaders.
Morsi’s office condemned the killings.
Shiite Muslims make up just one percent of Egypt’s population which is primarily Sunni Muslim.
Sunnis have traditionally opposed Shiism, which teaches that many of the Prophet Mohammed’s companions revered by Sunnis were corrupt and usurped power from his rightful successor and cousin, Ali.
Shiites are also frequently accused of being under the influence of Shiite-majority Iran. -AFP