We report a case of agenesis of the gallbladder with the presence of a small dysmorphic cyst, along the bed of the gallbladder and cystic duct. The patient presented to us with a suspected diagnosis of atrophic and sclerotic gallbladder that was not seen on ultrasound examination, indicating the need for cholecystectomy. The patient's medical history report mentioned agenesis of the left kidney. The existence of a congenital abnormality led us to suspect the inability to visualize the gallbladder was probably due to a possible agenesis of the gallbladder. The patient was investigated with magnetic resonance cholangiopancreatography (MRCP), that confirmed the suspected diagnosis and avoided unnecessary surgery. The hypothesis of anomalous development or agenesis of the gallbladder should always be suspected when the gallbladder is not visible on ultrasound imaging, especially in patients with other congenital anomalies. We believe that in all these patients, MRCP must always be performed to help make decisions on the treatment protocol.