A subset of minimal change nephrotic syndrome was reported to be induced by autoantibodies against nephrin. We have reported that rats injected with murine anti-nephrin antibody showed proteinuria. However, its precise pathogenic mechanisms remain unclear. The initiation events of podocyte disturbance caused by anti-nephrin antibodies were analyzed using an in vivo rat model and in vitro assays with rat isolated glomeruli and human cultured podocytes. To elucidate the role of ephrin-B1 at the slit diaphragm, podocyte-specific ephrin-B1 knockout mice were analyzed. Nephrin-binding ephrin-B1 at slit diaphragm interacted with Par6 and interfered with the binding of Par6 with cdc42. Anti-nephrin antibodies caused the phosphorylations of nephrin and ephrin-B1 in a TRPC6-mediated Ca2+ influx-dependent manner. Phosphorylated ephrin-B1 was dissociated from nephrin and also from Par6. Par6, released by ephrin-B1, interacted with cdc42. The binding of Par6 stabilized cdc42 and consequently promoted cdc42 activity. Elevated cdc42 activity increased calcineurin activity and consequently activated Snail. The activated Snail negatively regulated the mRNA expressions of the slit diaphragm functional molecules, nephrin and ephrin-B1. Elevated cdc42 activity activated Stat3 independently of calcineurin. The activated Stat3 brought on the expression of claudin1, a tight junction molecule. The altered expressions of these molecules at the protein level were observed in the rat anti-nephrin antibody-induced nephropathy when the rats showed proteinuria. Ephrin-B1 at slit diaphragm suppresses cdc42 activity by preventing the interaction of Par6 with cdc42 and functions to keep the specialized phenotype of podocytes. Elevated cdc42 activity induced by the binding of Par6, released by the phosphorylated ephrin-B1, is a critical initiation event leading to proteinuria in the anti-nephrin antibody-induced nephropathy.