Abstract: A 14 year old female was admitted to Elshab Medical Teaching Hospital, Khartoum, Sudan. As informed by the father, there was a history of cough for 2 months, chest pain for 2 months and breathlessness for 3 weeks. An intercostals drainage tube was administered to alleviate the condition and to relief pneumothorax. The patient was referred to thoracic surgery unit for thoracotomy of the left side of the chest. The second X-ray and MRI revealed the presence of a large hydatid cyst in the lower lobe of the right lung. The hydatid cyst was situated at the junction of the ventrolateral aspect of the upper lobe and dorsolateral aspect of the lower lobes of the right lung. Because of the deteriorating condition of the patient, thoracotomy was initially performed in the right side of the chest to remove the giant hydatid cyst. A week later, thoracotomy was also performed to remove a ruptured pulmonary cyst from the upper lobe of the left lung, which was found infected with secondary bacterial organism. An incidental cyst was also observed in the liver. Thus, this patient represents a case of multiple hydatid cysts. Conventional bacteriological examination revealed isolation and identification of Pseudomonus stutzeri from the infected hydatid cyst. Molecular characterization revealed that the cyst is of genotype 6 (G6) strain of Echinococcus granulosus as detected by polymerase chain reaction (PCR)-based assay.