The incidence of diaphragmatic hydatid cysts, isolated or involving other organs, is very rare. Preoperative diagnosis of complicated hydatid cysts located at the diaphragm is challenging. In some cases with a liver cyst the cyst cannot be detected during laparotomy. In this article, we report three diaphragmatic cyst cases who were treated surgically in our clinic within the past 10 years. Cystectomy and primary diaphragm repair using posterolateral thoracotomy were applied to all three cases with an intraoperative diagnosis. There was a ruptured diaphragmatic cyst in only one case, while other cysts were intact and located in multiple organs. A preoperative diagnosis of diaphragmatic hydatid cysts is difficult, and standard treatment is surgery for all intrathoracic hydatid cyst cases.