Rhabdomyosarcoma is the most common childhood sarcoma that occurs in the soft tissues of the head and neck, genitourinary system, and extremities. While this tumor may also be seen in young adults, it is distinctly unusual to see this neoplasm beyond the fifth decade. The use of fluorescence in situ hybridization (FISH) probes on fine-needle aspiration material for chromosomal analysis to detect chromosomal translocations are not well established. Herein we present a case of metastatic alveolar rhabdomyosarcoma originating in the nasal sinus and recurring in the neck of an adult man 5 yr after his initial presentation. The ThinPrep® smear demonstrated isolated malignant tumor cells similar to his previous histologic material. The cytologic findings of alveolar rhabdomyosarcoma were confirmed utilizing a dual color break apart FISH probe which identified the FKHR translocation on the cytospin preparation prepared from a ThinPrep® vial and processed as a cytospin preparation. In addition to routine and immunocytologic staining, we demonstrate that aspirated tumor cells can be analyzed using a FISH probe to identify specific chromosomal abnormalities. Diagn. Cytopathol. 2006;34:704–706. © 2006 Wiley-Liss, Inc.