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Persistent and/or recurring muscle pain, especially in the hamstrings and rotator cuff in the shoulders can be a sign of vitamin D deficiency. If you notice pain in these or other areas, keep a record of the duration and intensity of the pain for a certain period of time. That way you can rule out temporary muscle pain or soreness from sleeping in the wrong position, for example. The more acute and prolonged the muscle pain, the more likely it is that you're deficient in vitamin D. Make sure you consult your doctor to confirm.