A Micro ATX motherboard is smaller in dimensions than an ATX motherboard and, therefore, will have fewer expansion slots. At most, you could have 3 PCI slots on a microATX board and many will only have 2 PCI slots, while a many full ATX boards will have 5 PCI slots.
The critical issue in deciding which motherboard to get is your computer case. "Full tower" ATX cases will always accommodate ATX motherboards. Most, but not all, Mid-tower cases will also accommodate ATX motherboards. However, mini-tower cases will most likely only accommodate microATX boards, although some will accommodate ATX boards.
A microATX board can be often be installed in a full or mid tower ATX case; however, I suggest you verify this before buying a microATX board to put in a full or mid tower ATX case. If you do this type of installation, you'll just have some slot openings on the back of your case that will never be used.
