Vitamin D3, combined with its nuclear receptor, regulates more than 900 genes, which is the reason why its effect is pleiotropic. Among other effects, it influences the immunological system. Its deficit may be one of the environmental factors taking part in the development of auto-immunological diseases. The studies reveal that, among others things, inflammatory bowel diseases occur in higher latitudes, with lower exposure to solar radiation and with decreased production of vitamin D3 in the skin. Patients with inflammatory bowel disease have vitamin D3 deficiency more frequently. The application of vitamin D3, especially among adults with inflammatory bowel diseases, positively influences bone turnover markers and mostly due to its influence on immunological processes, vitamin D3 may be useful in the treatment of the primary health condition. It is necessary to determine the dosage range, as well as the optimal level of vitamin D3 metabolite-25OHD3, where the immunosuppressant effect is the best, with no toxic effects. Studies of vitamin D3 analogues deprived of the hypercalcemic influence, but with other merits of the basic substance remaining intact, are particularly promising.