Is a CPU Fan header 3 or 4 pin?

4-pin fans are better because then the mobo can automatically control the fan speed. 3-pin fans tend to run a lot higher than they need to.
 
Usually 4. You can connect a 3 pin fan to it though.

4-pin fans are better because then the mobo can automatically control the fan speed. 3-pin fans tend to run a lot higher than they need to.

I'm going to combine these two posts and make a detailed answer. A CPU motherboard header is traditionally a 4-pin header. Attaching a fan to this header will cause the fan to fluctuate rotation speeds in response to fluctuations in CPU temperature. As you have probably guessed, higher RPM results from higher CPU temperature and vice verse. Both 3-pin and 4-pin motherboard headers have a plastic tab that fits into the slot on a fan header. No matter which pin count and hole count combination you have, the fan header and motherboard header should fit together and produce a powered fan.

Now if you're using a regular case fan (attached to the chassis directly), you wouldn't want to use a CPU fan header to power the fan if you have the choice. As stated above, regular motherboard headers supply full power (12V) to the fan header, and thus maximum fan speed. Case fans shouldn't fluctuate in speed for various reasons.
 
I'm going to combine these two posts and make a detailed answer. A CPU motherboard header is traditionally a 4-pin header. Attaching a fan to this header will cause the fan to fluctuate rotation speeds in response to fluctuations in CPU temperature. As you have probably guessed, higher RPM results from higher CPU temperature and vice verse. Both 3-pin and 4-pin motherboard headers have a plastic tab that fits into the slot on a fan header. No matter which pin count and hole count combination you have, the fan header and motherboard header should fit together and produce a powered fan.

Now if you're using a regular case fan (attached to the chassis directly), you wouldn't want to use a CPU fan header to power the fan if you have the choice. As stated above, regular motherboard headers supply full power (12V) to the fan header, and thus maximum fan speed. Case fans shouldn't fluctuate in speed for various reasons.

In that case, is it necessary to have a fan plugged into a cpu header? (water cooling...)
 
I assume you're asking that question because you want to plug your radiator fans into either different motherboard headers, or a fan controller?

Anyway

Whether it will work or not depends on your specific motherboard, some will POST fine without detecting a CPU Fan, others won't. You'll just have to try it. :)
 
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