Vitamin D has important influences on many phases in the innate branch of the immune system (cellular, complement, antimicrobial peptides, lectins, non-antibody producing aspects of immunity), and also in the adaptive branch of the immune system (antibody-producing aspects of immunity). The adaptive branch of the immune system has two major phases. The effector phase involves antibody production while the regulatory phase involves removal of B cells producing antibodies that cross-react with self-cells. The antibody-antigen lock and key fit isn’t always exact. Even healthy people have self-reactive B cell clones. Similarity between a “foreign” antigen and a host cell membrane element may exist or an antibody may overlap the membrane portion of a neoantigen-membrane complex. When B cells with these self-reacting or self-cross-reacting antibodies are stimulated to mass divide and produce their antibodies, they must be destroyed by the regulatory immune cells (Tregs) to minimize self-injury. Imbalance or dysfunction in the regulatory phase of the adaptive immune response is the major mechanism of autoimmune diseases in humans. Interestingly, several sensitive areas of the body, the brain, anterior chamber of the eyes, and testes, are devoid of adaptive immune responses. The risk of collateral damage from antibody production in these areas is too great.