We report the rare case of an isolated gallbladder with cystic duct agenesis that was misdiagnosed as acute alithiasic cholecystitis. We underline the inaccuracy of currently used diagnostic tests and the importance of making a correct preoperative diagnosis to avoid a needless surgical procedure. Based on the rare and incidental nature of this congenital anomaly, we discourage an extensive routine diagnostic workup, but rather, suggest a careful clinical and diagnostic evaluation of the patient who has symptoms suggestive of biliary tract disease. We conclude that in patients with gallbladder and cystic duct agenesis surgery might be useless and risky when performed by the laparoscopic approach. On the other hand, the awareness of the laparoscopic surgeon of the problems posed by this anomaly and a careful review of currently available diagnostic tests can prevent unnecessary laparotomy and minimize the risk of complications.