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Since cross is coming and gravel is coming (have had multiple emails recently referencing "the fall gravel season") and fall is coming and all of that, and all of that means disc brakes more and more each year, it's time to go through the differences between center lock and 6 bolt disc brakes.
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Because we'd be dumb not to accommodate as much personal consumer preference as possible, almost all of our builds are available with either 6 bolt or center lock. There are certain hubs like Chris King where some axle types (12mm) are only available for center lock and some are only available with 6 bolt (15mm). In these cases, we show the limited options on the relevant product page to prevent confusion. We also do our Aivee MP2 based builds in center lock only, just to keep inventory manageable.
A good place to start is this video that we did a while ago. Bear in mind that when we do videos, it's basically "have an idea, turn on the cameras and go" so these aren't quite as produced as a GCN video. Please excuse that. With that done, the biggest thing to point out is that both center lock and 6 bolt hubs and rotors will work with your brakes. Yes, if you have disc brakes, you can use either format. The hub's rotor interface is only an attachment method between the hub and the rotor. So long as that rotor is delivered to the place where your brakes expect and want and need it to be, which both formats do, the brakes themselves don't care at all whether your hubs and rotor are 6 bolt or center lock. If need be, you can shim your rotors using either commonly available 6 bolt rotor shims or our super genius, exclusive center lock rotor shims. These allow you to set your rotor alignment precisely so that swapping wheels happens without any adjustment needed and no rotor rub.
If you have center lock hubs, you can use 6 bolt rotors. There are adapters that are cheap, readily available, and effective. Many people are reluctant to change from 6 bolt to center lock hubs because they have a bunch of 6 bolt rotors hanging around that they don't want to turn into junk. Adapters make that a non-issue.
Centerlock rotors are typically a few dollars more than most 6 bolt rotors. That is because center lock rotors need to be 2 piece (there's an aluminum center part for the hub attachment and then a steel part for the actual business end of the rotor). The better 6 bolt rotors are also 2 piece, so they are the same cost. Two piece rotors seem to stay true and resist warping a little better, plus the aluminum does a good job of dissipating brake heat.
Centerlock rotors are generally easier and more error proof to install. One simple lock ring versus 6 small bolts to get cross threaded or stripped or lost or whatever else happens to these things.
We carry the appropriate rotors for any disc type anyone reading this is likely to have or need in the store, which again helps make it easy. The only critical thing you need to know is rotor diameter, which is printed on your existing rotors if you have them, or will be in your brake and/or bike specs. For almost everyone reading this, you have either 140 or 160mm rotors. Some of you will have 180s on your mountain bikes. If you do downhill, you might have bigger rotors.
So the center lock versus 6 bolt debate is actually pretty straightforward. All else being equal, my personal preference is center lock, but once they're on and tuned, you really don't notice too much one way or the other.