Kaposi's sarcoma is generally believed to be a non-neoplastic hyperproliferation because it may regress spontaneously and its spindle cells lack features of typical tumor cells, such as aneuploidy, nuclear atypia, and permissive growth in cell culture. A fundamental characteristic of neoplasms is clonality, in that they arise from clonal replication of a single cell whereas reactive processes are derived from polyclonal proliferation. We used an X chromosome inactivation assay to determine the clonality of Kaposi's sarcoma nodules from patients with AIDS-related disease. The assay is based on a methyl-sensitive restriction digest followed by PCR amplification of the highly polymorphic androgen receptor gene. Two of three evaluable cases had a monoclonal pattern of inactivation, and the third case had a clonal expansion of cells with an altered microsatellite repeat sequence. These data suggest that Kaposi's sarcoma (at least in the AIDS setting) is a clonal neoplasm.