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I am relatively new to running, a year in now, having come across from cycling and have built up from the real basics (run 1 min, walk 1 min) to doing about 15 miles a week between 2 runs. Recently (last 4 weeks) I have started to get a dull pain in my right ankle, the pain is very localised and appears to be in/on the bone on the inside of the joint. It occurs during longer runs and I do get residual pain afterwards but it generally disappears during the following day. I can happily run with the discomfort but know that this probably isn't the best course of action if I don't want to end up with a running related injury.
I recently had my stride etc examined and as a result I bought a new pair of trainers and orthotics, before that I had been running in a pair that a friend had given me.