In recessive polycystic kidney disease (PKD), renal collecting duct cystogenesis and bile duct dilation are associated with increased cell proliferation. Pathogenic mechanisms are undefined. Bone morphogenetic proteins signal via intracellular SMAD1 to decrease cell proliferation during normal collecting duct formation. These studies test the hypothesis that SMAD activity is decreased in kidney and liver in murine models of PKD. In the B6 cpk/cpk model of recessive PKD, and Balb bpk/bpk model of recessive PKD and biliary dysgenesis, immunoblot and immunohistochemistry demonstrated decreased renal PSMAD1 at P10 when cysts were fully formed. Balb bpk/bpk mice demonstrated decreased PSMAD1 immunostaining in bile ducts. These abnormalities were absent at P1, despite the presence of pathogenic changes. Unaltered PSMAD1 levels in Balb/B6 cpk/cpk model of recessive PKD and liver dysgenesis suggest that SMAD1 activity is modulated by genetic background. We conclude that decreased PSMAD1 may contribute to the proliferative cystic phenotype in murine PKD.