Since you are running long distances, you could be developing a stress fracture in your heel. A stress fracture is an incomplete break in the bone caused by wearing down of a bone. The wearing down occurs from any activity you do throughout the day. It could be walking to the office, or up a flight of stairs, or from your car to your house. In this case, you are adding an extra stress from the running that you do. The stress fracture occurs because your bone is not able to rebuild itself before you run each day. This causes a deficit in bone, leading to the painful incomplete break in the bone. This is a common condition found in distance runners because of the amount of strain they place on the bones in their legs and feet.
It could also be an Achilles tendon strain. The Achilles tendon connects your calf to your heel, and is the rope-like part just above your heel. This could become damaged with repetitive running -- especially if you are running up hills frequently -- because it places the most workload on the Achilles.