Five cases of chordoma, diagnosed by fine-needle aspiration (FNA) biopsy, are presented. Four cases were histologically confirmed, and in one, immunocytochemical and ultrastructural studies were performed on both the aspirate and tissue specimen. Four cases presented as sacral masses, while in the fifth case, a destructive lesion of the clivus extended into the soft tissues of the lateral neck. A spectrum of cytomorphologic features was encountered including the presence of abundant microtissue fragments and cells in a dissociate pattern, often with abundant metachromatic extracellular matrix. Stellate and cuboidal cells often contained intracytoplasmic vacuoles of varying sizes. Intranuclear inclusions, mitotic figures, and anisonucleosis were prominent features of several cases. Immunoperoxidase studies on a single case demonstrated cytoplasmic staining for low- and high-molecular-weight cytokeratins, vimentin, and epithelial membrane antigen, while glial fibrillary acidic protein and carcinoembryonic antigen were negative. Ultrastructural features included the presence of mitochondrial endoplasmic reticulum complexes, occasional desmosome-like junctions, and abundant extracellular matrix adherent to the tumor cells. We believe the cytomorphologic findings are characteristic and, when taken in concert with immunocytochemical and ultrastructural studies, allow differentiation of chordoma from other primary or metastatic neoplasms occurring in bone. As demonstrated in our series, chordoma is often an unsuspected diagnosis. We believe that FNA biopsy of these lesions can lead to a correct preoperative diagnosis and may also be utilized to document recurrence and thus facilitate the evaluation and management of patients with these lesions.