The counts include hate crimes as well as firearms offenses.
The suspect, Robert Bowers, has requested a jury trial to determine whether he is guilty of the 44-count indictment pressed against him by prosecutors Wednesday.
Bowers was indicted on 44 criminal counts for the shooting and faces the death penalty.
He was flanked by two USA marshals as he entered a federal courtroom Thursday wearing red prison scrubs, a bandage on his left arm and shackles on his hands and feet.
Authorities say Bowers raged against Jews during and after the deadliest anti-Semitic attack in American history.
Bowers remained jailed without bail.
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The panel issued the indictment as funerals continued for the victims.
Students from the Yeshiva School of Pittsburgh, pay their respects as the funeral procession for Dr.
Many school families were gathered for a bar mitzvah Saturday at their synagogue, Shaare Torah, listening to sirens screaming by outside.
"You could hear siren after siren", said school CEO Dan Kraut.
Fienberg's sons, Anthony, of Paris, and Howard, of Vienna, Virginia, said she spent five years caring for their father as he battled cancer, then, after his death a few years ago, devoted more of her time and energy to Tree of Life.
They were joined by Mr Trump's daughter Ivanka and her husband, Jared Kushner, as well as Tree of Life Rabbi Jeffrey Myers and Ron Dermer, Israel's ambassador to the US.
Three children killed when struck at Fulton County bus stop
Aerial footage shows a damaged truck after a fatal crash at a school bus stop in Fulton County, Indiana, on October 30, 2018. It's believed the three children, twin boys, 6, and a girl, 9, were from the same family, Slocum said .
Services for Mel Wax and Irving Younger are also scheduled for Wednesday.
On their arrival in Pittsburgh, the Trumps entered the vestibule of the synagogue, where they lit candles for each victim before stepping outside.
Following a spate of politically motivated pipe-bomb mailing to prominent Democrats, the shooting heightened national tensions days ahead of elections next Tuesday that will decide whether US President Donald Trump will lose the Republican majority he enjoys in both houses of Congress.
"The President was very warm, very consoling". We were treated so warmly. If nothing else, pray for their recovery from this terrible anti-Semitic attack, and pray that it's the last we'll see in our lifetimes. Some community leaders had asked Trump not to make the trip.
The city's Jewish community began burying its dead Tuesday as thousands of mourners attended services for a beloved family doctor and two brothers.
Younger, whose funeral will also be held at Rodef Shalom, was remembered as a doting grandfather.
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Rabbi Eli Wilansky lights a candle after a mass shooting at Tree of Life Synagogue in Pittsburgh, Oct. 27, 2018.