Wendy’s or Subway? Depends which way you vote.

June 13, 2012, 4:30 PM UTC

FORTUNE — Everybody knows we’re living in hyper-polarized times. The American people are more divided today by political affiliation than even race or class, an unprecedented if unsurprising development exposed by a recent Pew Research Center study.

Now we’ve got proof those differences spill over heavily into what both Democrats and Republicans like to eat, watch, and drive. A new survey from the neuro-insight firm Buyology, released exclusively to Fortune, shows the two sides divided over a majority of 200 brands across a range of categories.

Some of the splits make intuitive sense: Democrats like to watch Animal Planet, while Republicans click over to the History Channel. Others are tougher to figure: Democrats prefer Wendy’s (WEN) and the NFL, Republicans go for Subway and Major League Baseball.

A common thread, Buyology CEO Gary Singer posits, is whether consumers would rather cede decision-making power to a central authority — a Democratic tendency — or see that power distributed, the favored Republican approach.

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Take chain restaurants. At Wendy’s, menu options are prepackaged into meals, and customers typically order by number; Subway patrons, on the other hand, are practically forced to customize their meals as they walk their sandwiches down an assembly line. “What Democrats are responding to is somebody smart making choices for them that makes their lives better and easier, and fundamentally what Republicans are responding to is the ability to make an individualized choice,” Singer says.

He sees the same dynamic at work when it comes to professional sports. Republicans have a deeper connection to baseball not simply because it’s “as American as apple pie,” but also because the sport’s central authority is more hands-off, allowing huge payroll gaps that have engendered the rise of super-teams like the Yankees, Phillies and Red Sox. The NFL, by contrast, “is more democratic, more legislated, more centrally controlled.”

It’s a provocative thesis, and Singer acknowledges its simply conjecture. But he’s got science to back up the results. The Buyology study is not the first to try to decipher how partisan allegiance reflects on brand preference. A recent study by auto-research firm Strategic Vision, for example, found when it comes to cars, Democrats favor fuel-efficiency (their top pick: the Honda Civic Hybrid) while Republicans go for size and power (top pick: the Ford Mustang convertible).

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But Singer’s effort breaks ground by using neuro-marketing techniques to plumb respondents’ subconscious minds, where researchers believe they can see past cognitive noise to reveal people’s true feelings. The method involved asking 4,000 respondents to answer quickly — think Malcolm Gladwell’s Blink — and tossing replies that were either too slow or suspiciously fast. In each category, respondents chose between every possible head-to-head match-up of the included brands, so what emerged was a ranking of their connection to each, from first to last.

For the most part, naturally, they disagreed. Democrats favor Sony (SNE) for electronics, Progressive (PGR) for insurance, Starbucks (SBUX) for coffee and Wii for gaming. Republicans respectively opt for Sharp, Allstate (ALL), Dunkin’ Donuts (DNKN), and XBOX.

But some notable exceptions suggest effective marketing can forge bipartisan consensus behind a brand. Apple (AAPL), which abandoned its “Mac vs. PC” ad campaign in 2009 after a four-year run, is no longer a guerilla-minded upstart challenging an entrenched industry. The evidence for that is not just in the company’s $539 billion market cap, but in the fact that Democrats and Republicans both list it as their favorite technology brand.

They likewise agree on Visa (V), Google (GOOG), and, perhaps surprisingly, Coca-Cola (KO). It was Pepsi (PEP), after all, that raised eyebrows after the 2008 presidential election with a new campaign that appeared to echo President Obama’s message. Singer speculates that Coke has broken through the political divide with brand positioning aimed at promoting happiness. And as Geoff Colvin notes in the current issue of Fortune, Pepsi’s marketing hasn’t exactly distinguished itself in recent years.

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Singer, who’s provided branding and management advice to Intel, McDonald’s, and the New York Stock Exchange, sees insights in the results for both politicians and corporations. The brands themselves could better understand “the subtle differences between them and their competitors and develop stronger attachments to their users.”

For pols, the study offers further confirmation of a trend identified by the Pew report: Republicans and Democrats are further apart than they’ve ever been on the proper role for government in American life. As Singer says, “At a deep level, there’s a philosophical difference between Republicans and Democrats, and what Democrats are looking for is a central body to help make the world we live in a little better, and what Republicans are advocating is more laissez-faire, local, let the people work it out.”

It’s a lesson President Obama, for one, is inclined to heed as his drive for reelection gears up. As he told the crowd at a Baltimore fundraiser on Tuesday, “you’ll never see a sharper contrast” between the parties than in the upcoming campaign.