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I can not find the dimensions of the Core i3 stock cooler anywhere.

Will a Core i3 stock cooler fit in a 2U rackmount case?

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Even if it did, you wouldn't want to use it. Rackmount gear is designed to intake from the front and blow out the back, stock Intel coolers blow top-down. This isn't a big deal in desktops, because of the extra space, but it makes a big difference in a rackmount setup. – MDMarra Jun 17 '10 at 2:10
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I think it fits. The core i3 stock cooler is about 6-7cm tall and you have 88.1mm in a 2U case. Considering the motherboard is raised a little bit, the fan should fit marginally. But as mentioned by MarkM, you won't want to do that.

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