Chocola defeated Tony Zirkle, an attorney, Navy veteran, and frequent candidate, in the Republican primary on May 2, 2006, by 70% to 30%. Zirkle, who said he was "willing to debate the idea of returning the guillotine and lynch mob for those who prey on children under the age of 12", was unable to get Chocola to debate him on that or any other subject.
Donnelly raised about $1.5 million to Chocola's $3.2 million. In mid-August, in a report on National Republican Congressional Committee planned spending, the Associated Press reported that "the GOP has not reserved advertising time to aid Rep. Chris Chocola in Indiana even though Democrats plan to spend at least $700,000 to win the district. House Republicans have told Chocola that he must fend for himself, given his personal wealth and his ability to raise large amounts of money."
A poll released in mid-June by the Donnelly campaign showed Donnelly leading 48% to 38% with 14% undecided. The campaign did not release all of the poll findings. A poll released six days later, taken by the South Bend Tribune, showed the race to be at the margin of error with Donnelly at 46% and Chocola at 41%. The telephone poll interviewed 400 likely voters who were asked whom they would vote for "if the election were held now".
On August 16, the Cook Political Report changed the rating for the race from "Lean Republican" to "Toss-Up", saying "Despite a significant fundraising advantage over Democrat Joe Donnelly, which has helped fuel a barrage of negative attack ads, incumbent GOP Rep. Chris Chocola looks more like an underdog than the frontrunner." Also in August 2006, Larry Sabato's Crystal Ball, a Web site run by the University of Virginia Center for Politics, added the race to their "Ferocious Forty" list of the 40 most competitive House races in the nation.
On November 7, 2006, Chocola lost his congressional seat to Democratic candidate Joe Donnelly, whom Chocola had defeated in 2004. The final tally showed Chocola losing by a 54–46 margin, almost an identical reversal of his fortunes in 2004. The election had a much lower turnout than the previous campaign, and the difference appeared to come in St. Joseph County. Historically a Democratic stronghold, Chocola lost it by only a few hundred votes while cruising to victory in 2004. In 2006, however, Donnelly won the county by nearly 14,000 votes, garnering 58% of the vote in what is by far the most populous county of the district.
Indiana's 2nd congressional district election, 2006
Julia Carson had held this Congressional seat based in urban Indianapolis since 1997, and had always won by comfortable margins. Republicans hoped to take the seat in the 2006 elections after redistricting made the 7th slightly more Republican, though Democrats still held the advantage.
Dickerson ran an aggressive grass-roots campaign, defeating the party-endorsed candidate, Ronald Franklin, and two other candidates in the Republican primary on May 2, 2006. He gained further support as the campaign progressed, with an October poll shocking observers of both parties when it showed Dickerson narrowly leading Carson 45% to 42%. Carson dismissed the poll, saying that she always polled more strongly than expected on election day. She was proven correct, winning her sixth term on November 7, 2006.