Celiac disease is a chronic small intestinal immune-mediated enteropathy precipitated by exposure to dietary gluten in genetically predisposed individuals and represents a major health issue. The immune mediated response results in villous atrophy of the small intestine with subsequent malabsorption. The classic mode of presentation is that of a malabsorption syndrome resulting in deficiencies of macro and micronutrients. The gluten-free diet is the only treatment currently available for this disorder. The aim of this special report is to elucidate and explain the various nutritional deficiencies seen in newly diagnosed patients with celiac disease and while on the gluten-free diet. Though initiation of the gluten-free diet results in improvement of symptoms and most deficiencies, certain nutritional limitations are associated with the gluten-free diet.