Nineteen House Democrats refused to vote for Pelosi as speaker, baring the lingering wounds from last fall's bitter elections that cost their party 64 House seats.
As Boehner took the gavel, he wiped away tears and said the people voted to end business as usual.
With ceremonies wrapped in tradition, members of the House and Senate were sworn in for the 112th Congress. Vice President Joe Biden gave the oath of office to senators.
Republicans vowed to use their new House majority to battle President Barack Obama on health care, spending, taxes and other issues.
In the Senate, lawmakers moved almost immediately to a debate over filibuster rules in which Democratic and Republican leaders accused each other of obstructing progress and trying to game the parliamentary system.
In the House, children and grandchildren of new lawmakers fidgeted, temporarily lending lighter moments to a chamber certain to see fierce debates and partisan votes in the next two years. House Republicans, for instance, plan to vote within days to overturn Obama's 2010 health care overhaul, but they acknowledge it's a symbolic gesture because the Senate will not concur.
The Associated Press contributed to this report.