[7] Bilbray ran in the 2006 special election to fill the vacancy in California's 50th congressional district caused by the resignation in December 2005 of fellow Republican Duke Cunningham, who pleaded guilty to felony charges of conspiracy and tax evasion, and subsequently went to jail.

Four days before the election, businessman Alan Uke, one of the major Republican candidates, ran an attack ad accusing Roach of outsourcing thousands of jobs at the expense of American workers.

He then faced the top vote getters of all the other parties in a runoff election on June 6, 2006: Democrat Francine Busby, Libertarian Paul King, and William Griffith, an independent.

The Republican Party considered this a bellwether race because this district had "the perfect storm in favor of the Democrats" according to Ken Mehlman, the RNC Chairman at the time of the special election.

With the advantage of incumbency and the Republican edge in registrations in the district, Bilbray was initially a clear favorite to win in November.

[15] Running unopposed in the June primary, Bilbray overcame a strong challenge from Democrat Nick Leibham in the November 2008 general election.

Democrats thought they had a chance at winning the district due to the hostile environment plaguing Republicans in general, and shifting demographics locally.

A runoff between Bilbray and Port of San Diego Commissioner Scott Peters, a Democrat, was held on November 6.

The initial vote was very close, so that a winner was not declared until ten days after the election as provisional ballots were counted.

In response to requests to District Attorney Bonnie Dumanis, by the local Democratic Party and neighbors of the congressman, a San Diego County grand jury was convened to investigate claims against Bilbray's declared residency for the special and general elections in 2006.

[20] During the 109th Congress Bilbray served on the House Armed Services, Veterans Affairs and Government Reform Committees.

During his first term Bilbray co-authored legislation that led to the transfer of the Mount Soledad Veteran's Memorial from the City of San Diego to the federal government.

Bilbray voted in agreement with President George W. Bush 93% of the time, and as a result was given a 93% Presidential Support Score by CQ Politics in 2006.

Bilbray almost always has voted for free trade agreements in the past years, specifically with Korea, Colombia, and Panama, all of which passed.

[25] In 2011, he voted for the National Defense Authorization Act for Fiscal Year 2012 as part of a controversial provision that allows the government and/or the military to indefinitely detain American citizens and others without trial.