Congenital anomalies of the liver, biliary tree and pancreas are rare birth defects, some of which are characterized by a marked variation in geographical incidence. Morphogenesis of the hepatobiliary and pancreatic structures initiates from two tubular endodermal evaginations of the most distal portion of the foregut. The pancreas develops from a larger dorsal and a smaller ventral outpouching; emergence of the two buds will eventually lead to the fusion of the duct system. A small part of the remaining ventral diverticulum divides into a "pars cystica" and "pars hepatica", giving rise to the cystic duct and gallbladder and the liver lobes, respectively. Disruption or malfunctioning of the complex mechanisms leading to the development of liver, gallbladder, biliary tree and pancreas can result in numerous, albeit fortunately relatively rare, congenital anomalies in these organs. The type and severity of anomalies often depend on the exact moment in which disruption or alteration of the embryological mechanisms takes place. Many theories have been brought forward to explain their embryological basis; however, no agreement has yet been reached for most of them. While in some cases pathological evaluation might be more centered on macroscopic evaluation, in other instances small biopsies will be the keystone to understanding organ function and treatment results in the context of congenital anomalies. Thus, knowledge of the existence and histopathological characteristics of some of the more common conditions is mandatory for every pathologist working in the field of gastrointestinal pathology.