Many of the nerves that come the spinal cord in the neck have branches that send fibers to the shoulder; irritation of these nerves, because of the way nerves work (often causing a phenomenom called referred pain) can cause shoulder pain when the problem exists elsewhere.  For instance, you have probably heard of people who are having a heart attack who report having pain in the left arm; this is an example of referred pain.  Referred pain occurs because the limb buds of the embryo develop into arms and legs, pulling the nerves along as the buds grow; the referred pain happens in patterns in part determined by whatever other structures developed in the limb bud or even in the precursors to the bud in the long axis of the spine (like the heart or esophagus).  Also, most of the shoulder nerves come from the 5th and 6th cervical nerve roots, which are the levels most commonly effected by ruptured discs or pinched nerves.  A good history and exam are very helpful in sorting out the problem.  MRI is extremely helpful as well, as can be nerve conduction studies.

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