There are two basic fan designs common now. The older one uses three pins (and wires) for connection, and those can ONLY be controlled for speed by a mobo fan header that uses Voltage Control Mode (aka DC Mode). If this type of fan is connected to a header that uses PWM Mode, it will always run at full speed.
The newer design is 4-pin fans (with 4 wires). These are controlled best by a header that uses the new PWM Mode for control; however, for backwards compatibility, these fans also CAN be controlled by a header using DC Mode.
The design of the wiring and connectors of these two types allows you to plug either type of fan into either type of header. Further, they are designed so that you can only plug them in one way, so you can't do it wrong. Electrically, the signals on the first three pins are VERY similar, which is why there is some backwards compatibility. The fourth pin is used only for the new PWM signal used by 4-pin fans; 3-pin fans cannot use that signal and do not connect to it.
There are four ways that mobo headers MAY be designed to deal with this mix of two possible fan types. And watch for this: the CPU_FAN header usually has some way of dealing with both types, but the SYS_FAN headers for case ventilation
fans often are not so flexible. Also be aware that these options are set for each header separately, not one master setting. Note also that VERY often all the headers have four pins, but this does NOT tell you how the control Mode works, because all possibilities can be done on a 4-pin header.
1. The header may claim to be able to detect whichever fan type is connected to it and adjust its control Mode automatically to what is needed. Most often this system also allows you to specify one particular control Mode rather than allowing automatic adjustment.
2. The header may not do its own automatic adjustment, but allows you to select the correct Mode in BIOS Setup.
3. The header may have only one control Mode already set and offers no option to change that.
4. The header may claim to work with either fan type but not actually offer any way to adjust its control Mode. Most commonly such headers actually are using only Voltage Control Mode and not sending out any PWM signal on the fourth pin at all. This will always work for 3-pin fans. For 4-pin fans they are making use of the backwards compatibility design of that fan type that CAN be controlled this way, even though it is not the ideal way. This is not a problem EXCEPT when you want to use a 4-pin fan HUB to connect several fans to one mobo header. Almost all such Hubs require that the header supply the PWM signal, and also require that the fans plugged into them be of the 4-pin design.
You should be aware that there are some mobos that have fan headers with NO control capability, irrespective of how many pins they have. They merely provide full voltage to the fan which always will run at full speed. These headers are most useful for devices such as pumps that should run full speed all the time, anyway. Note, too, that some mobos have a special header for a fan called PWR_FAN. This was originally intended only for use with a special set of wires coming from certain PSU units to allow the PSU to send to the mobo the speed signal of its internal fan, so it really is not a good place to connect any other fan.