"What is critical is that we stand together at this dark time as one body," he added. "We need to rally around our wounded colleague, the families of the fallen, and the people of Arizona's 8th District. And, frankly, we need to rally around each other."
The Capitol Police has beefed up security on Capitol Hill and across the country, members of Congress say they are taking extra precautions amid fear of copycat attacks.
In a bipartisan move that hasn't been seen in some time, Boehner and House minority leader Nancy Pelosi, D-Calif., held a conference call to brief members on the Arizona shooting and the Congressional response.
Members were reminded to take common-sense precautions and inform local law enforcement of their events.
At least two members of Congress, Heath Shuler, D-N.C., and Jason Chaffetz, R-Utah, say they're not taking any chances. The two told Politico they'll be packing guns when in public in their home districts.
There will be another bi-partisan security briefing on Capitol Hill by the Capitol Police, Sergeant-at-Arms and the FBI when members of Congress return Wednesday.
Doctors are hopeful that Giffords, who remains in intensive care, will recover and say that she is responding to basic commands, but they caution that the 40-year-old is not yet completely out of the woods.
Loughner, who was charged on four counts Sunday, will make his first court appearance in Phoenix today in front of Magistrate Judge Lawrence Anderson.
The president has been careful not to ascribe any political motive to the killings, instead cautioning against doing so. This weekend, Obama spoke to Giffords family as well as the family of Gabe Zimmerman, the congresswoman's 30-year-old employee who died on Saturday. A 9-year-old girl born on the day of the Sept. 11, 2001 terrorist attacks was also killed.
ABC News' Ariane de Vogue, Jonathan Karl and Jake Tapper contributed to this report.