The question of whether there are inflammatory changes in colorectal biopsy specimens is frequently asked, especially when the patient reports diarrhea or when the mucosa is reddened on endoscopy. The pathologist first has to find out whether there is, in fact, an increase in the inflammatory infiltrate of the colorectal mucosa which warrants the diagnosis of inflammation. If so, the second challenge is to ascertain the etiology of these inflammatory changes, in particular to differentiate between infectious and non-infectious causes. In principle, we can distinguish forms of colitis with distinct morphological hallmarks confirming the diagnosis (e.g. microscopic detection of the causative organism, as well as lymphocytic or collagenous colitis) from other forms of colitis which have a characteristic pattern of findings not necessarily allowing to deduce the etiology (e.g. infectious colitis without microscopic evidence of the germ vs. inflammatory bowel disease). The present article discusses the pathomorphology and differential diagnosis of the most important forms of bacterial colitis.