Inflammatory bowel disease (IBD) is an inflammatory disorder in which intestinal homeostasis is disrupted for some reason. Among them, ulcerative colitis (UC) and Crohn's disease (CD) are frequently referred to as IBD in the narrow sense, characterized by relapse episodes and remission periods. The differential diagnosis of IBD involves a broad spectrum of inflammatory or infectious diseases that mimic UC and/or CD, as well as others that may complicate existing IBD. Accordingly, these differential diseases and modifying factors should be considered in their pathological diagnosis, and a careful diagnosis should be made in close collaboration with clinicians. Here, we provide a pathological overview of UC, CD, and their differential diseases, as well as IBD-associated cancers, demonstrating their typical gross and histological features. Further, we introduce a pathological scoring system for biopsy specimens to diagnose IBD that may potentially be integrated into clinical practice.