When you walk in high heels, the center of your body mass is pushed forward, causing your spine to arch forward out of its ideal alignment. This skeletal change is immediately visible on an X-ray. The misalignment puts uneven pressure on your rear and front intervertebral discs, which can cause back muscular and joint pain, as well as pinched nerves.
In the same way your spine moves out of alignment when walking or standing in heels, so do your hips. To keep your balance in heels, you have to compensate by pushing your hip bones forward. This causes increased strain on your hip flexor muscles, which can eventually cause them to shorten.
Heels often cause a tighter fit in the toe area as gravity forces the toes to be pushed into the narrower front of the toe box. As toes are pressed together at the tip of the shoe, you may develop a bony growth at the base of the big toe (a bunion), which causes it to angle in toward the other toes.
As feet slide further into the narrow toe box of a heel, the smaller toes begin to bend into a claw shape. After repeated exposure to this position, the toes may become unable to straighten, even when you're barefoot.