Cases of intrathoracic extropulmonary hydatid cysts are very rare. We identified 13 patients with intrathoracic extrapulmonary hydatid cysts in our clinic over 12 years. Four patients had extrapulmonary cysts only; nine patients had both intrapulmonary and extrapulmonary cysts. Cysts were identified in the pleural space, extrapleural region, diaphragm and chest wall. Thoracotomy was used in all patients, and extrapulmonary lesions were removed by cyst extirpation from surrounding tissue or by pericystectomy. In one patient with chest wall involvement, partial rib resections were performed because of rib destruction. In two patients with liver cysts passing through the diaphragm to the thorax, the diaphragm was cut, cysts on the liver roof were removed and then the diaphragm was repaired. There was no mortality, morbidity, or disease recurrence during the post-operative period in any of the 13 patients. We conclude that these rare cases give a new insight into hydatid cyst pathophysiology.