Topoisomerase II (topo II) is an enzyme that affects replication, transcription, and chromosome segregation. It serves as a target for several useful antichemotherapeutic agents, such as etoposide (VP-16) and teniposide (VM26). Monoclonal antibody topo IIalpha (Clone JH2.7; Neomarkers, Union City, CA) specifically identifies the alpha isoform of topo II. Using this antibody in an immunohistochemical analysis, we studied differential expression of topo II in a variety of thyroid lesions. The topo II labeling index is defined as the number of topo II staining positive nuclei divided by the total number of tumor cells counted multiplied by 100. An average of 1,000 cells were counted in each case. The average labeling indexes for anaplastic carcinoma (7.8), tall cell variant of papillary carcinoma (4.8), follicular carcinoma (2.6), Hürthle cell carcinoma (3.4), and medullary carcinoma (2.4) were much higher than for papillary carcinoma (0.76), follicular adenoma (0.65), Hürthle cell adenoma (0.32), and normal thyroid (0.1). This study suggests that immunohistochemical analysis of topo II correlates with thyroid tumor histology; it is more frequently expressed in tumors that are associated with aggressive clinical behavior. It may help to define a role for anti-topoisomerase drugs in treatment of aggressive thyroid neoplasms.