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Since this topic comes up quite a bit, I decided to put something together to help out anyone that is having a little trouble understanding the differences and to help to choose the right one. This will apply to AR-15 rifles, and more specifically to iron sights, red dot sights, and the low powered variable scopes (1x4 scopes) in tactical applications, not precision shooting.

This means that the reticle and the iron sights will line up. The irons and the red dot are pretty much the same height. I say pretty much because there is no such thing as "ABSOLUTE". The height for Iron sights is just under 2.6". Most of the Absolute/Regular Co-Witness mounts on the market such as Larue, ADM, Bobro, etc, are actually around 2.75", which is close enough to the iron sight height.

This is where the iron sights appear in the lower 1/3 window/section of the optic. Most of the Lower 1/3 Co-Witness mounts on the market such as Larue, ADM, Bobro, etc, are around 3".

Front and rear flip-up BUIS is the most versatile set-up and gives you the greatest flexibility.
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These are generally the lightest, simplest, and generally the most rugged.
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This is one of the most popular set-ups because most AR's come with the fixed front sight base, which is pinned and very rugged.
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Now that I explained some of the terms and some of the different available options, let's determine the best height to use. If you read some of these types of threads, you will read where guys will post that the lower 1/3 co-witness is best because it allows you to keep your head in a more upright position, which is ideal for CQB type work. The upright head position, IMHO, is the correct position. Unfortunately, we are not 1-size fits all. In other words, we are not all 6'3" tall. I learned that the hard way and it cost me $200 in mounts. I have always used the absolute/regular co-witness because it was very comfortable for me. My head was in the upright position when I shoot with irons or with the Aimpoint or EOTech with an absolute/regular co-witness. So one day I purchased an Aimpoint and was talked into getting the lower 1/3 mount because my head would be in an upright position. My first range session with these lower 1/3 co-witness mounts, proved to be a huge mistake. I was no longer able to even get a cheek weld position. It was more like a chin weld position. And shooting from the prone was very painful for my neck because I had to lift up my head to obtain a proper "chin weld" position. My friend on the other hand had no problem with the lower 1/3 mounts. I'm 5'7" tall and he's 6'2" tall. So what I recommend to determine what the best height FOR YOU is without going out and spending a couple of hundred dollars on mounts is to just look through your iron sights and determine where your head is. If you look through your irons and you r head is relatively upright, then you may want to go with the absolute/regular co-witness mounts. I should mention that the sight height is more critical when using a magnifier or a regular scope. When I just use an Aimpoint or EOTech, even if it is in the lower 1/3 co-witness, it isn't that much of a problem for me because the reticle in the red dot scopes floats around. Confused yet? It gets better.

What if you use fixed front and rear BUIS or a fixed front and flip-up rear BUIS? Then you to deal with another factor that doesn't exist with the flip-up front and rear BUIS. Some people, no matter how hard they try, they just can't get used to having the front sight in the way. It can be very annoying, especially with a regular 1x4 scope because the reticle just sits right on top of the front sight post. At least with a red dot, you can slightly raise your head and the reticle will clear the front sight post and not be as annoying.

If you have/use the front and rear flip-up BUIS, I recommend that you just determine what height is best for you based on your head position. If you have a fixed front BUIS/Sight, you have to first determine the proper height based on your head position, and then, if you determine that you would be better off with the absolute/regular co-witness height, then you have to determine if you can put up with the front sight being in the way.