Congenital agenesis of the gallbladder and cystic duct represents a rare anomaly of the biliary system. It likely results from an embryologic mishap in the development of the hepatobiliary bud and can occur with other associated malformations. We report the case of congenital absence of the gallbladder and cystic duct incidentally found during laparoscopy in a 44-year-old Caucasian female. Based on the clinical presentation and ultrasonography findings, the patient was presumed to have symptomatic cholelithiasis and chronic cholecystitis. A laparoscopic cholecystectomy was planned. After introducing the laparoscope, the gallbladder and cystic duct were absent and the procedure aborted. Gallbladder and cystic duct agenesis was confirmed by magnetic resonance cholangiopancreatography. We describe here the difficulties with diagnosis and pain management, and review the literature of this rare pathology.