Basaloid squamous cell carcinoma (BSCC) is an unusual but well-established entity, primarily in the upper aerodigestive tract, composed of basaloid cells associated with dysplastic to neoplastic squamous cells, and characterized by an aggressive and rapidly fatal course. To date, BSCC originating in the trachea has not been reported. In this article, the authors describe the clinical, gross, and microscopic pathologic, histochemical, and immunohistochemical features of two cases of BSCC arising in the trachea. Features distinguishing this entity from other, more common tumors of the trachea, including metastases and direct extension from other sites of origin, are also discussed.