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Unfortunately very few people know that the inflammation from RA can affect your tendons which can feel like muscle pain and in fact cause your muscles to hurt.  RA can rupture your tendons and also cause your tendons and ligaments to be unstable.  This could be just what you rheumatologist says, a flare.  However, if you have any doubts speak to your primary physician and he may be able to run tests or send you to a specialist.  Nobody knows your body as well as you, so if you are not convinced it is a flare then you owe yourself a second opinion.  Good luck and best wishes!