Surgical treatment of bile duct cysts remains the mainstay to reduce cyst-related complications and risk of malignancy. Optimizing treatment outcomes is dependent upon a thorough preoperative evaluation and selecting the appropriate intervention. This review summarizes the recent progress in the evaluation and treatment of bile duct cysts, particularly in relation to contemporary operative approaches. Ongoing efforts continue in optimizing the evaluation, classification and management of bile duct cysts. The risk of cholangiocarcinoma is not limited to the bile duct cyst itself and appropriate management and surveillance is paramount. Recent advances in laparoscopic and endoscopic equipment have paralleled an increasing interest in minimally invasive approaches in the management of patients with bile duct cysts. Favorable results of laparoscopic approaches are increasingly reported and suggest the feasibility of this technique in select patients. Although the surgical premise of resection has not changed for the treatment of bile duct cysts, there has been an increasing utilization of minimally invasive approaches. Results thus far are promising, but long-term, controlled data is needed before this approach can be considered standard.