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3-pin is strict voltage control, 4-pin can be controlled by PWM (much more precise RPM control.)

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If it's labelled as a 3/4-Pin* it may either be a 4-pin or a 3-pin to 4-pin molex. 4-pin fan connectors will work on 3-pin fan headers (the pins on the motherboard). 3-pin is power and speed sensor (RPM). 3-pins require voltage regulation to change speed, that is to say you must increase and decrease the voltage. 4-pins are PWM as Kobathor said. PWM stand for Pulse Width Modulation. In case you don't know how PWM works, think of a cardiac (heart) monitor. PWM sends a pulse to the fan, each time it peaks it sends a pulse of 12 volts to the fan (12v in this specific application; PC usage). The pulse frequency changes to adjust the speed.

 

(Bad) example of PWM

_ = 0 volts, - = 12v

_-_-_-_-_

 

Edit

3/4-pin | A slash is sometimes used to me "to" so 3-to-4 pin, just explaining why I mentioned the 3-pin to 4-pin molex.

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