Multiloculated thymic cysts are uncommon lesions that can be either acquired or associated with malignancies. This report describes the fine‐needle aspiration (FNA) cytology of a mediastinal seminoma with prominent cystic change, confirmed by surgical pathology examination and ancillary studies performed on both the cytology and tissue specimens. The FNA cytology revealed clusters of malignant oval‐to‐polygonal‐shaped cells with large oval nuclei possessing prominent nucleoli set in a pale‐to‐eosinophilic cytoplasm. These cells were surrounded by a dense lymphoid infiltrate along with a few noncaseating granulomas. The large malignant seminoma cells stained positive for placental alkaline phosphatase (PLAP) and negative for both low molecular and broad‐spectrum cytokeratin. The differential diagnosis of malignancies associated with thymic cysts is presented. To the best of our knowledge, this is the first report of aspiration cytology of a mediastinal seminoma associated with a multilocular cyst. Diagn. Cytopathol. 1999;20: 224–228. © 1999 Wiley‐Liss, Inc.