Microscopic enteritis (ME) is the stage of microscopic and sub-microscopic changes (microenteropathy) associated with the symptoms of gluten sensitive enteropathy leading to micronutrient deficiencies. It is characterized by subtle mucosal abnormalities without prominent inflammation, villous effacement, erosions or ulcerations on conventional light microscopy. The intraepithelial lymphocytes are usually in normal range <25/100 enterocytes (microenteropathy) or increased (lymphocytic enteritis). ME is the entity behind atypical forms of CD previously known as potential and latent CD. Systemic inflammation predominantly is found to be engaged in pathophysiology of micro-nutrient deficiency even in absence of macroscopic mucosal changes.