The suspect has been identified as Robert Bowers, police officials say.
Four officers were also shot in the attack at the Tree of Life Congregation in Pittsburgh's Squirrel Hill neighborhood.
Police spokesman Chris Togneri said police have no more information at this time because they were still trying to clear the building and determine if any more threats exist.
The synagogue is located at the intersection of Wilkins and Shady avenues. The tree-lined residential neighborhood of Squirrel Hill, about 10 minutes from downtown Pittsburgh, is the hub of Pittsburgh's Jewish community.
Pittsburgh Mayor Bill Peduto said all residents of the neighborhood are required to stay inside their homes until further notice.
Jeff Finkelstein of the Jewish Federation of Greater Pittsburgh told WPXI that organization's security officer has notified all JCC synagogues and that they are on modified lockdown.
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President Donald Trump said he was monitoring the shooting. In a tweet, Trump encouraged people to shelter in place and said "looks like multiple fatalities."
Pennsylvania Gov. Tom Wolf called the shooting an "absolute tragedy."
"We must all pray and hope for no more loss of life," Wolf said. "But we have been saying "this one is too many" for far too long. Dangerous weapons are putting our citizens in harm's way."
In 2010, Tree of Life Congregation - founded more than 150 years ago - merged with Or L'Simcha to form Tree of Life (asterisk) Or L'Simcha.
The synagogue is a fortress-like concrete building, its facade punctuated by rows of swirling, modernistic stained-glass windows illustrating the story of creation, the acceptance of God's law, the "life cycle" and "how human-beings should care for the earth and one another," according to its website. Among its treasures is a "Holocaust Torah," rescued from Czechoslovakia.
On my way to Pittsburgh. Headed to the scene at Tree of Life Synagogue shooting.— Governor Tom Wolf (@GovernorTomWolf) October 27, 2018
The suspect is in custody.
We are providing local first responders with whatever help they need.
Its sanctuary can hold up to 1,250 guests.
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Finkelstein said local synagogues have done "lots of training on things like active shooters, and we've looked at hardening facilities as much as possible."
"This should not be happening, period," he told reporters at the scene. "This should not be happening in a synagogue."
Just three days before the shooting, Rabbi Jeffrey Myers posted a column on the congregation's website, noting that people make time to attend funerals, but not for life's happy occasions.
"There is a story told in the Talmud of a wedding procession and a funeral procession heading along parallel roads, with the roads intersecting," Myers wrote on Wednesday. "The question asked is: when they meet at the fork, which procession goes first, funeral or wedding? The correct answer is wedding, as the joy of the couple takes precedence. In fact, the funeral procession is to move out of sight so that their joy is not lessened."
Myers ended his column with words that now seem all too prescient.
"We value joy so much in Judaism that upon taking our leave from a funeral or a shiva house, the customary statement one makes (in Yiddish) is 'nor oyf simches' - only for s'machot," Myers wrote. "While death is inevitable and a part of life, we still take our leave with the best possible blessing, to meet at joyous events. And so I say to you: nor oyf simches!"
SWAT prepping rifles as Pittsburgh active shooter situation continues at Tree of Life synagogue in Squirrel Hill pic.twitter.com/eimPxyRACP— Beau Berman (@BeauWTAE) October 27, 2018
We'll update this story as new information comes into the ABC30 newsroom.