Squats - Knees

When I do back squats, my knees tend to go forward near the end of the concentric movement. I find it quite hard to prevent them from moving forward.

I read in the Rippetoe book a way to prevent this (I know this isn't probably the best way) is to move the knees to the right position in the first 1/3 of the squat movement, and then when you squat, the knees won't move that much more forward. I've just started to do that in my squats.

The question I want to ask is there any side effects from doing this? For example knee injuries?

I'll paste the quote from his book here.

Rippetoe - Starting Strength 2nd Edition

The answer is to learn to squat with the knees in the proper place, and to move them
correctly during the descent One approach is to make all of the forward knee travel occur in the
first third or half of the descent . From the top, shove the knees forward and out to the place they
will end up, just in front of the toes, and then the rest of the movement will consist of the hips
moving back and down. Make two movements out of this for a couple of reps, and then reduce
this to a smooth single motion (fig. 2-51) .

Most people are going to have to let their knees go out over their knees at least a little bit.  I use a wider stance than most people, and this still happens to me.  It's not really that big a deal.

Just make sure you are using as low a bar position as possible and are squatting back, and not down.  Initiate the movement by pushing your hips back, and THEN breaking at the knees.  Also, use flat soled shoes like Chuck Taylors.  Not only will all of this allow you to squat pain-free, but your numbers will be higher from the increase recruitment from your hips and hamstrings.

If all else fails, get some knee sleeves, or if you really need some knee protection, some wraps.

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