Vitamin D is a prohormone that is primarily responsible for calcium homeostasis and maintaining bone health, but recently the role of vitamin D in cellular proliferation and differentiation, immunomodulatory functions, and gut microbiome modulation has been well established. Several gastrointestinal conditions such as inflammatory bowel disease, celiac disease, pancreatic diseases, chronic liver diseases, malabsorptive bariatric surgery, and gastrointestinal malignancy predispose to vitamin D deficiency with resultant adverse clinical outcomes. Early diagnosis and adequate vitamin D supplementation are imperative to prevent detrimental outcomes. The purpose of this chapter is to comprehensively focus on vitamin D physiology and functions, association of vitamin D with specific gastrointestinal diseases, and evidence-based recommendations for evaluation and treatment of vitamin D deficiency.