Want to protect your knees. Squat deeper!

Nice squat but this
guy needs a tan

Deep Squats Help Protect Your Knees 

Right off the bat lets get one thing straight. A squat is when the hip drops below the top of your knee and the back remains straight (straight and vertical are not the same thing). Anything above this is not a squat and I can not vouch for its safety. It has long been thought that it was safer for your knees if flexion was reduced. This has led to people stopping well above parallel all in the name of safety. Then of course we have all witnessed the performance of squats where depth is reduced in direct relation to weight going on the bar. This has nothing to do with safety and a lot more to do with impressing your friends.  The very act of reducing this range of motion while increasing resistance has probably lead to more knee and back injuries, in and outside of the gym, than any amount of properly performed squats with any amount of weight.

Partial squats stress the quads and the knee joint without activating the supporting structure of the glutes, adductors and hamstrings. In the full squat position the anterior force provided by the quads is balanced by the posterior force provided by the hamstrings. So in simple terms the quads put forward tension on the knee  and the hamstrings put tension in the opposite direction. Without this balancing tension a shearing force is produced on the patellar tendon and tendinitis (or worse) is likely to occur sooner or later.  The squat of course takes the blame but you have not been doing squats. The hamstring group of muscles does not come into play before parallel so they can do nothing to counteract this shearing force produced by the quads as they try to to grind the weight to a screeching halt before it staples you to the ground. 

Having a load on has
really improved my form

Doing your squats to a full, deep position protects your knees outside of the gym as well.  ACL injuries are very common in sports.  The ACL is primarily involved in preventing the tibia from sliding forward relative to the femur.  The hamstrings do the same thing.  If the hamstring have not strengthened from correct range of motion squatting, they cannot help the ACL support the knee and the ligament is left to take all of the strain.  Strong  hamstrings can do such a good job of helping to support the knee that it is possible to do a correct full squat with a damaged ACL while a quarter or half squat will cause sever pain.  If more high school and college football/hockey/soccer players were made to squat to correct depth it would likely go a long way in preventing ACL injuries on the field. Back injuries would also be reduced as athletes would not be able to load their spines with nearly as much weight. Its rare to see a high school student that can squat 225 properly but it is not uncommon to see one doing some bastardized form of a squat with 400+ while the rest of the team spots him.

Many times knee injuries and hamstring pulls are blamed on athletes being too "quad dominate" when in fact their quads are not too strong, the hamstrings are too weak.  Spend your time in the squat rack wisely and get every rep below parallel. It may surprise you initially how little weight you can do but I promise you it will pay off in the long run, both in how you look and how you perform.