By Tory Newmyer, writer

FORTUNE — As the morning-after pundits sifted through the results of the New Hampshire primary on Jan. 11, a quieter fight over the future of the campaign was playing out in a Washington, D.C. courtroom. Lawyers for Chris Van Hollen, a Democratic congressman from Maryland, along with a team of campaign-finance reform advocates, had come to sue the federal government. They want Uncle Sam to require that independent political groups spending millions on television ads — outfits like the U.S. Chamber of Commerce — reveal their donors. But even the suit’s backers say it’s a peashooter against the tank of newly unlimited money rolling into the 2012 elections.

That’s thanks to the two-year-old Supreme Court decision in the Citizens United case lifting constraints on outside spending — and the anti-regulation Republicans hobbling the Federal Election Commission from following up with transparency rules. The new normal has given rise to so-called super PACs: political groups all-but-officially linked to candidates that are able to raise huge sums from donors who, with a little paperwork, can remain nameless. Beyond the headlines, the groups have already made a real mark, in some cases outspending the campaigns they support by 2-to-1 or more.

Restore Our Future, the super PAC backing Mitt Romney focused its withering fire on Newt Gingrich in Iowa, reversing the former House Speaker’s rise there. A fund supporting Gingrich responded in kind in South Carolina with the help of a $5 million infusion from casino magnate Sheldon Adelson. The barrage helped force another hairpin turn in the campaign, knocking Romney onto defense over his years at Bain Capital. The spending continues apace in Florida, where the fund backing Romney has reportedly booked several million dollars worth of television time, while the Gingrich group has reloaded with another $5 million contribution from Adelson’s wife.

So far, the super PACs have spent an estimated $32 million in the 2012 campaign. But we won’t know where the bulk of that money came from until the end of the month, thanks to slick accounting maneuvers used to delay filing past the first four contests. Even then, donors could remain anonymous if they choose to route their checks through straw-man organizations. There’s some precedent for that: Last summer, Restore Our Future accepted a $1 million check from a shell corporation. Under intense media and watchdog pressure, a Bain colleague of Romney’s later acknowledged founding the company.

Even before the rise of super PACs, outside groups had been taking advantage of weaker disclosure requirements to hide more donors. In the 2010 cycle, fully 44% of outside spending was anonymous, up from 1% in the 2006 elections, according to the Center for Responsive Politics. Says Meredith McGehee, policy director of the Campaign Legal Center, which is supporting the Van Hollen suit, “The stakes here are free and fair elections.”

A shorter version of this article appeared in the February 6, 2012 issue of Fortune.