We point out the issue of differential diagnosis regarding the finding of ectopically localised thymic tissue (a thymic cyst) in the neck. Thymic tissue can be found anywhere along its developmental tract of descent, from the angle of the mandible to the upper mediastinum. Disruption of the thymic descent can result in ectopically/abnormally localised islets of accessory thymic tissue, which may undergo cystic changes, as described in a case report by Sun et al . This anatomical variation of the thymus may be clinically misinterpreted as a neoplasm or other congenital anomalies as a branchial cyst, lymphatic malformation or cystic hygroma. The present editorial focuses on the challenge of establishing a diagnosis of ectopically localised tissue of thymus often presented as a lateral cervical mass, especially in the case of cystic variation/degeneration of this thymic tissue. We summarise hypotheses on the origin of such congenital cervical thymic cysts from the point of view of evolutionary history and embryology. We also discuss lesser-known facts about the anatomy, histopathology and developmental biology of the thymus as one of the most enigmatic organs in the human body.