Bile duct cysts are a rare medical condition and are more frequent in children. However, the disease is becoming increasingly common in adults. The modified Todani classification, which is based on anatomical characteristics, is the current standard classification method. However, this classification does not take the following factors into consideration: different epidemiology, pathogenesis, risk of malignant transformation, clinical and imaging aspects, and different therapeutical approaches for all the bile duct cysts. Thus, some clinicians denied its clinical significance and viability. Moreover, some rare variants (i.e., cystic duct cysts) of bile duct cysts were initially not included and were subsequently categorized as type VI. Although it clusters different diseases, the Todani classification of bile duct cysts should also be used in clinical practice because it is simple, reproducible and widely agreed upon, thereby allowing an appropriate comparative analysis between different series of patients who are classified based on this scheme. Exceptional, cystic duct cysts should be included in the Todani classification (as a subtype of type II BDC rather than as a "new" type VI) so that the gastroenterologists, radiologists and surgeons are aware of this variation.