Vitamin D is a cyclopentane polyhydrophenanthrene compound involved mainly in bone health and calcium metabolism but also autophagy, modulation of the gut microbiota, cell proliferation, immune functions and intestinal barrier integrity. The sources of vitamin D include sunlight, diet and vitamin D supplements. Vitamin D3, the most effective vitamin D isoform is produced in the human epidermis as a result of sunlight exposure. Vitamin D undergoes two hydroxylation reactions in the liver and kidney to reach its active form, 1,25-dihydroxyvitamin D. Recent studies highlighted a complex spectrum of roles regarding the wellbeing of the gastrointestinal tract. Based on its antimicrobial effect, it was recently indicated that vitamin D supplementation in addition to standard eradication therapy might enhance eradication rates. Moreover, it was suggested that low levels of vitamin D might also be involved in the acquisition of infection. In terms of celiac disease, the negative effects of vitamin D deficiency might begin even during intrauterine life in the setting of maternal deficiency. Moreover, vitamin D is strongly related to the integrity of the gut barrier, which represents the core of the pathophysiology of celiac disease onset, in addition to being correlated with the histological findings of disease severity. The relationship between vitamin D and cystic fibrosis is supported by the involvement of this micronutrient in preserving lung function by clearing airway inflammation and preventing pathogen airway colonization. Moreover, this micronutrient might exert anticatabolic effects in CF patients. Inflammatory bowel disease patients also experience major benefits if they have a sufficient level of circulating vitamin D, proving its involvement in both induction and remission in these patients. The findings regarding the relationship between vitamin D, food allergies, diarrhea and constipation remain controversial, but vitamin D levels should be monitored in these patients in order to avoid hypo- and hypervitaminosis. Further studies are required to fill the remaining gaps in term of the complex impact of vitamin D on gastrointestinal homeostasis.