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Vitamin D and its deficiency are becoming a subject of great interest in recent years. In addition to the well-known role of vitamin D in maintaining bone health, evidence from recent years are accumulating in favor of its importance in the functioning of the immune system. The association between vitamin D deficiency and autoimmune diseases has been supported by epidemiological studies, demonstrating higher prevalence of vitamin D deficiency among autoimmune patients, in comparison to the general population. Vitamin D was also associated to various autoimmune diseases in both molecular and interventional studies; among the associated diseases are: systemic lupus erythematosus, type 1 diabetes mellitus, multiple sclerosis and others. In this review, relevant literature on the association between autoimmunity and vitamin D deficiency will be reviewed and discussed, as well as a summary of important recommendations for vitamin D supplementations in autoimmune patients.