Microscopic colitis (MC) is a chronic inflammatory bowel disease, encompassing a triad of chronic diarrhea, normal endoscopy and characteristic histological findings. MC embraces two histological subtypes described as lymphocytic colitis (LC) and collagenous colitis (CC). The diagnostic criteria of MC were established several years ago and the histological description of LC and CC was based almost exclusively on heamatoxylin-eosin (HE) stained sections. Since the establishment of the diagnostic criteria, important changes have occurred in the concept and diagnostic methods of MC: the emergence of the entity "microscopic colitis incomplete" (MCi), comprising collagenous colitis incomplete (CCi) and lymphocytic colitis incomplete (LCi) and pathologists' increasing use of special stains in everyday diagnostics. The diagnostic challenges of today are threefold: which stains to apply to properly distinguish between MC, MCi and slight inflammatory changes, how to handle cases of diagnostic uncertainty and how to minimize inter observer variability. The views of this article are from the pathologist's perspective. We describe the changes in criteria and diagnostic methods of MC occurring over time, discus pathologists' diagnostic challenges and suggest how these can be met: by automated image analysis of tissue sections and by international collaboration under auspices of the PRO-MC collaboration, a European collaboration on the disease course of MC.