As long as your foot biomechanics are ok and the shoes you wear are well typed to your feet, the most common cause in an adrenal dysfunction. This can occur if overtraining or too far anaerobic. Can also come from poor diet (too high sugar/stimulant intake) or from general stress.

It could be fibromyalgia. I had the same prob especially first thing in the morning, but since I have been taking a supplement for magnesium it seems to have gone. Check out About.com for the FM

Sorry if my post is a little vague, but I'll do my best. Also, all apologies for potentially hi-jacking your thread.

I've recently been running a fair amount 2-3 times awake during ball hockey, soccer, and at the gym. Since over the last few weeks I've also been experiencing rather crippling pain in my right heel/achilles area. Intense pain as soon as I let the area rest for more than a minute or two... and yeah, the worst pain is in the mornings too.

The thing is that I've had this condition since I was in my early teens and perhaps earlier. I for the life of me can't remember what the doctors had mentioned as the culprit, but I have a vague memory of him mentioning a short tendon and the heel itself tearing in to the tendon. I'm not even sure if the latter is possible...?