The PAX genes encode a family of transcription factors that control development within the neural, myogenic, lymphoid, and a variety of other lineages. These proteins are postulated to regulate expression of gene products that function in the control of cellular processes are fundamental to the development of cancer, and thus genetic alterations of these genes may contribute to neoplastic development within these lineages. In support of this premise, several PAX genes have been shown to be targets of consistent chromosomal translocations associated with specific tumor types. The t(2;13) and t(1;13) translocations associated with the myogenic soft tissue cancer alveolar rhabdomyosarcoma fuse portions of the PAX3 or PAX7 gene with a portion of the FKHR gene to generate novel fusion proteins. The t(9;14) translocation associated with the B cell tumor lymphoplasmacytoid lymphoma juxtaposes the PAX5 gene into the vicinity of the IGH locus to deregulate PAX5 expression. This review will examine the molecular basis of these translocations and the role of altered function or expression of paired box transcription factors in the process of tumorigenesis.