Distinguishing ulcerative colitis (UC) from Crohn's disease (CD) is normally based on evaluation of a variety of clinical, radiologic, serologic and pathologic findings, the latter in biopsy and/or resection specimens. Unfortunately, some patients with IBD show overlapping pathologic features of UC and CD, which makes definite distinction between these two disorders difficult or even impossible. In most instances of uncertainty, the patient shows clinical and pathologic features of UC, but in addition, the patient's colon resection specimen reveals one or more CD-like features. In this setting, a diagnosis of indeterminate colitis (IC) is often rendered. IC is not a distinct disease entity, and, thus, it has no diagnostic criteria. The most common causes of uncertainty in IBD pathology that may lead to a diagnosis of IC in a colon resection specimen includes the presence of fulminant (severe and toxic) colitis, insufficient radiologic, endoscopic, or pathologic information (including analysis of prior biopsies) on the patient, failure to utilize major diagnostic criteria as hard evidence in favor of CD, failure to recognize unusual variants of UC and CD that may mimic each other, failure to recognize non-IBD mimics and other superimposed diseases that cause unusual pathologic features in a resection specimen, an attempt to distinguish UC from CD in mucosal biopsies of the colon and ileum, or an attempt to change the patients diagnosis (of UC or CD) based on pouch or diversion-related complications. Details of each of these causes of uncertainty are discussed, in detail, in this review article. A diagnosis of IC should never be made clinically or by pathologists based on evaluation of pre-resection colonic mucosal biopsies. Ultimately, the majority of indeterminate cases represent UC, and, thus, most of these patient can be treated safely with a colectomy combined with an ileal pouch anal anastomosis procedure.