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Abstract Background Intra-thymic bronchogenic cysts are a rare entity but should be considered in the differential of all non-invasive thymic masses. Case presentation We describe a 50-year-old patient who was found to have an incidental thymic mass on computer tomography of the chest. Non-invasive thymoma was suspected and a thoracoscopic thymectomy was performed. Final pathology revealed a bronchogenic cyst. Conclusion Intra-thymic bronchogenic cysts are extremely rare tumors of the anterior mediastinum. It should be considered in differential diagnosis of anterior mediastinal masses.