A case of sacrococcygeal chordoma with anaplastic features is presented. The diagnosis of the anaplastic component was first established by fine needle aspiration (FNA) biopsy, which demonstrated the sarcomatous elements as well as the physaliferous cells characteristic of chordoma. Subsequent histologic examination confirmed these findings. While the FNA cytologic findings of chordoma have been previously reported, this is the first case of an anaplastic chordoma diagnosed by FNA biopsy. The embryologic origin of this unusual tumor and its differential diagnosis are discussed.