Microscopic colitis has emerged as a major cause of chronic watery non-bloody diarrhoea, particularly in elderly females. The term is used as an umbrella term to categorize a subgroup of colitides with distinct clinicopathologic phenotypes and no significant endoscopic abnormalities: Lymphocytic colitis is defined by an increased number of surface intraepithelial lymphocytes, collagenous colitis by a thickened collagen band underneath the surface epithelium. There is increased inflammation in the lamina propria, but only little or no crypt architectural distortion. Incomplete and variant forms showing less characteristic features have been reported under different names. Differential diagnosis mainly includes resolving infectious colitis and changes related to the intake of drugs such as non-steroidal anti-inflammatory drugs. Substantial clinical and histological overlap between lymphocytic and collagenous colitis has been described, raising the suspicion that the conditions are two histological manifestations of the same entity, possibly representing different manifestations during the disease course or different stages of disease development. In this review we provide a practical approach for pathologists with focus on diagnostic criteria and differential diagnosis, discuss recent insights into the pathogenesis of disease and the relation to classical chronic inflammatory bowel disease, i.e. Crohn's disease and ulcerative colitis.