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NBC News and CNN projected soon after polls closed that Cruz would defeat GOP frontrunner Donald Trump.
Trump had repeatedly predicted that he would defeat Cruz in Wisconsin despite polls suggesting otherwise.
Cruz's win is especially important because it makes it more difficult for Trump to secure their party's nomination outright.
Trump is hoping to get the 1,237 delegates necessary to avoid a contested convention in July. If the real-estate magnate falls short of that number, a contested convention would allow anti-Trump forces to potentially coalesce against him.
Cruz became the clear favorite in Wisconsin after a series of Trump stumbles along the campaign trail. The Texas senator led Trump by nearly 5 points in the latest RealClearPolitics average of several polls ahead of Tuesday's vote.
The Texas senator is reportedly the only candidate holding an event in the Badger State following the election.
Trump is hoping to slavage a few of the 42 delegates at stake. Although winning the statewide vote guarantees Cruz 18 delegates, Trump can gain three delegates for each congressional district he wins. The data-journalism website FiveThirtyEight is reporting that Trump is "competitive" in two of the state's eight districts.
The next Republican primary, in New York, is on April 19.