What is the difference between a ATX motherboard and a Micro ATX aside the size?

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Mostly just the size. But the size effects how many PCI/RAM slots it has. So with a micro atx motherboard you would not be able to run three videocards, maybe not even two.

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ulfsark basically covered it but I wanted to add something.

if you look at an ATX mobo with some enthusiast features (not fully decked out, but not bottom of the barrel), and then look at a mATX with all those features, the mATX will be more expensive.

Big premium for feature-rich mATX boards, but similarly priced to ATX with less features.

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