Transcriptional regulation of podocyte gene expression in primary glomerular disease is poorly understood. In this study, we demonstrate a prominent role of members of the ZHX (zinc fingers and homeoboxes) family of proteins in regulating podocyte gene expression during the development of nephrotic syndrome. While studying mechanisms of glomerular disease, rat ZHX3 was cloned from a down-regulated gene fragment; its cellular localization, DNA binding, and transcriptional repressor properties were characterized; and its ability to influence podocyte gene expression directly or via ZHX1 and ZHX2 was studied. In eukaryotic promoters, ZHX3 bound to the CdxA binding motif. ZHX proteins were mostly sequestered in the non-nuclear compartment in the normal in vivo podocyte by virtue of heterodimer formation, and loss of heterodimerization was associated with entry into the nucleus. In experimental minimal change disease, ZHX3 was transiently down-regulated prior to the onset of proteinuria, and recovery of expression was associated with migration of ZHX3 protein into the nucleus and the development of proteinuria. This expression pattern mirrored the increased nuclear ZHX3 expression noted in vivo in the podocytes in human minimal change disease biopsies. In vitro, migration of ZHX3 protein into the nucleus during recovery from transient ZHX3 knockdown reproduced the gene expression profile of in vivo minimal change disease. Severe sustained knockdown of ZHX3 caused down-regulation of genes involved in focal sclerosis, including WT1, mediated mostly by increased nuclear entry of ZHX2 and ZHX1. In summary, ZHX proteins are major transcriptional mediators of podocyte disease.