Cystic changes of the thymus are rare lesions. In addition to their appearance in non-neoplastic congenital and acquired conditions, they have been seen in association with certain malignancies of the thymus. Our aim is to highlight the possibility of confusing between benign and malignant thymus cysts having different cure approach. We report two thymic cyst cases, one congenital ectopic condition, and the other one, a cystic thymoma. Investigations included blood counts, echograms, and computed tomography. The cysts were excised by mediastinal route and examined pathologically. The final diagnosis was made only after histopathological examination of the surgery biopsy revealing two types of cystic thymic lesions: congenital and tumoral. Because thymic cysts may present malignant transformation, they represent a diagnostic challenge that is resolved only by surgical excision and histological examination. Due to cystic changes masking tumoral features in these cases, thorough sampling is required to ensure that a malignancy is not overlooked.