Hydatid cysts located in the interatrial septum are especially rare but when they occur, they might cause intracavity rupture. We report on a patient with acute pulmonary embolism caused by an isolated, ruptured hydatid cyst on the right side of the interatrial septum. A 16-year-old-boy with an uneventful history was hospitalized for exercise-induced dyspnea and blood expectorations. Multiple and bilateral opacities were visualized on standard chest x-ray. Signs of right-sided hypertrophy were seen on ECG. Imaging findings led to the diagnosis of pulmonary embolism complicating cardiac hydatid cysts. An operation was performed through median sternotomy to remove the cardiac cyst. The pleural cavity was entered through the fifth intercostal space to withdraw lung hydatid cysts. Operative recovery was uneventful and the patient resumed his normal activities 19 months later. Prompt diagnosis and an appropriate surgical treatment prevented a potentially fatal outcome.