Question which fan header of the motherboard should the case fans be connected to ?

Oct 14, 2021
This seems to be a question I have seen many times. I would like to give my thoughts on this and I would like your opinions on this. I build high power audio amplifiers (300/400 watts/channel) where the requirements are 'different' so maybe I am influenced by their requirements so please bear with me.....

In my opinion, all the case fans should be connected to the fan header which is likely to register/detect the hottest part of the entire motherboard. This is because otherwise, if the fan head the fans are connected to is NOT the hottest detecting fan, all the case fans would be running at a lower speed than what the hottest part of the board should want the fans to be running at and therefore not cooling to the level it needs to be cooled.

This MAY end up obviously causing all the fans to be running at a higher speed than usual. But is that not the idea ? If there is a hot spot developing in the case, shouldn't the fans be trying to cool that specific hot spot ?

Having said that, how do we decide (or observe) where the hottest part of the board is and whether there is indeed a fan header very close to that area ? Maybe I am wrong but the answer to that maybe the CPU fan header. In your experience, is there any other part of the motherboard which may run hotter than the CPU ? In the new X570 based motherboards, is it possible that this specific chipset may actually run hotter than the CPU ?

Opinions are welcome.

fan header placement has nothing to do with reported temperatures or fan performance.
most fan headers are based on CPU temperature by default though many can be altered to read from the GPU, VRM, or other sensors on the motherboard.
and still others are set to run @ 100% for liquid cooling pumps.

the VRM on the motherboard is going to be the hottest section of the board itself.
with a case with good airflow and good cool air intake fans and exhaust fan(s), unless you have a very low quality motherboard, the VRMs shouldn't get warm enough to worry about.
the CPU & GPU will usually be quite a bit warmer though and therefore have their own cooling.
though many higher end boards actually include a small VRM fan.

with a lot of boards the CPU_FAN header has to be populated or the system will just show CPU Fan Error on the POST screen.
many times you can change the option in the BIOS to ignore this though.
but normally this header should be used for your CPU cooler's fans, not chassis fans.

your end goal should be to have a good cooler on your CPU,
enough cool air coming into the system to give everything an adequate amount,
and enough exhaust to make sure the warmed air is constantly being removed without sucking the cool air out before it gets to do it's job.

using quality PWM fans with good curve profiles in place for the CPU and the case is the best way to set it up.
which fan header of the motherboard should the case fans be connected to?
whichever case fan header is close enough to offer good cable management.
it will not matter which CHA_FAN / SYS_FAN / etc is used.
if you have more fans than headers available you can always get a nice fan hub and just use a single motherboard header to control multiple case fans.
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It is not correct that most fan headers are connected to the CPU temperature. In almost all mobos there are TWO main "groups" of fan headers. One group is the CPU_FAN header, and may include CPU_OPT, AIO_PUMP, and a few others. These all are normally set to use ONLY the temperature sensor for the CPU - most often the one built onto the CPU chip itself which sends out its signal on one chip pin. The second group is called SYS_FAN or CHA_FAN headers, and they are intended for use with the case ventilation fans. Normally they should be configured to use as their guide the mobo temperature sensor, a unit built into the mobo at a point where the maker has decided this is reasonably representative of the cooling needs ot the entire mobo (except the CPU that's already taken care of). These days it is common to offer in the configuration options of these headers the choices of the main mobo sensor, the CPU temp sensor, or any of several extra sensors at particular mobo points. Generally, these options are useful only if you plan to place a fan aimed at a special mobo component you want to devote one fan to.

You have hit upon the BIG dilemma in choosing NOT to use the normal "general" mobo temp sensor. How do you decide what the correct temperature for that sensor is? You see, the maker has already studied the temperature and cooling needs of many mobo components and has pre-programmed into the BIOS default configuration for those headers the correct temp target for that sensor. They ALSO have made a decision which of the many possible mobo components is the proper focus - that is, if THAT ONE is properly cooled then all the other important components also will be properly cooled. So by deciding NOT to use that sensor and its pre-programmed cooling parameters, you are deciding that you have MORE information that the mobo maker had, and know better. Now, doing this for ONE fan focused on one component may make some sense, but you still have to figure out the proper temp target for that part. But doing this for ALL of the mobo does not strike me as reasonable.

If your argument is: you can't cool too much, so use the hottest temp reading you can get, you do not need automatic temperature control. All you need is to connect ALL your case fans directly to a PSU 12 VDC output from a 4-pin Molex connector, and let them all run full speed all the time. I do NOT recommend that.
It is not correct that most fan headers are connected to the CPU temperature...
The second group is called SYS_FAN or CHA_FAN headers, and they are intended for use with the case ventilation fans. Normally they should be configured to use as their guide the mobo temperature sensor
well i've got 4 boards at this house; 2x ASUS, 1x AsRock, 1x Biostar.
all 4 of these by default have all of their sensors set to use CPU temp as their guide for fan control.

the fact that headers are designed to be used for case fans does not negate that they would be using a CPU temperature sensor for their source temp.
most manufacturers realize that this will be the warmest section of the system so use this sensor because they do not know where a header's corresponding fan may be placed on the chassis plus if the CPU's temperature is rising then more cool air should be brought into the system and more of the warmed air should be exhausted.

the ASUS & AsRock boards offer Motherboard / Chipset, VRM, GPU, & custom probes as options for their source temperature but the Biostar only allows for CPU as source.

so it would appear that four boards from over the last decade say that you are actually incorrect.
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