We present the case of a 38-year-old woman with a thymus cyst with an incidental tiny adenocarcinoma. Adenocarcinomas and adenosquamous carcinomas of the thymus or in thymus cysts have seldom been reported. These cases were overt invasive carcinomas. Our case is the first report on an incipient adenocarcinoma in a thymus cyst. It demonstrates the importance of thorough histological examination of cystic changes in the thymus, not only for the diagnostic classification of the lesion but also to ensure that a possible malignant change is not overlooked.