The review shows the relationship of vitamin D deficiency (VDD) with various forms of pathology of the gastrointestinal tract. The VDD prevalence in Russia has regional and age characteristics and reaches 42%. In addition to the key role as a regulator of calcium metabolism, which ensures the growth and formation of the structure of bone tissue, vitamin D was established to affect the course of various forms of pathology of the gastrointestinal tract. At the same time, it acts as a regulator of innate immunity. In other cases, the effects of vitamin D are aimed at activating anti-inflammatory factors, which determine its positive effect on the course of diseases through antioxidant action. Data on the VDD impact on the formation of various forms of intestinal pathology with an inflammatory and immune mechanism of development are presented. The authors point to the VDD impact in inflammatory bowel diseases. Regardless of the VDD primacy of inflammatory bowel disease, the correction of the VDD has a pronounced positive effect on the course of the disease.