Pretty much. There are standards for the motherboard and internal case form factors to prevent such problems. The most common form factor for a motherboard is the ATX form factor, and the most common form factor for a case is the ATX form factor. So if you get an ATX board and an ATX case, it will fit.
I believe that Intel recently tried to push a new BTX form factor (BTX boards and cases) that offered better cooling for their exteremely hot Netburst-based CPUs, but I suspect that those cases and mainboards will be fairly hard to find.
For the most part it's ATX, though there are some mini- and micro-ATX form factor boards out there, I believe that they will still fit in an ATX case.
If you have a full ATX case, you should be able to but almost any ATX motherboard in it. If it is a mini- or micro-ATX case, it will not take a full-ATX motherboard. Also, there are a few extended-ATX motherboards, usually marketed to the server market, that may not fit in most ATX cases. Those cases are pretty big, as they are also made to accomodate full length PCI cards as well. Again, full-lenght cards are mostly in the server/workstation segment, so you probably won't have to woory too much if this is for home.
You can find case reviews all over. I usually start with Tom's Hardware or AnandTech. It may help you find the case thats right for you, if you don't have one already. If you already have a case, take a look at how many expansion slots are available. It will give you a good indication of what size motherboard you should be looking for.
You want a Midi tower or bigger to fit a full size ATX motherboard.
Basically any tower with 3 (or more) 5.25inch rom bays and two 3.5inch (floppy type) bays should accomodate.
Smaller towers will restrict you to mini ATI motherboards.
Also I cannot stress enough, how important a good quality power supply is. That means ditch the generic (with case) PSU, unless it's quality ie: as supplied with Antec cases for instance.
Also note your motherboards power connection requirements (most new motherboards need a Version 2.0 or above 24pin power plug type with dual rail power) and of sufficient wattage for your parts.
Martin
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