Gene transfer into the mammalian kidney has proved difficult because of the structural complexity of the organ and its low mitotic index. This article describes the use of intra-arterially injected adenovirus to study gene transfer into the rat kidney in vivo. By pre-chilling the kidney, and incubating the virus with the kidney in the cold for extended periods of time, we were able to successfully transfer a beta-galactosidase (beta-gal) reporter gene into the vasculature without ischemic injury to the kidney. Transfer occurred largely in the cortex when cold was used alone, whereas with the use of cold and vasodilators, transfer was accomplished into the outer medulla in both the inner and outer stripes. In the Han:SPRD rat model of autosomal dominant polycystic kidney disease (ADPKD), gene transfer occurred into the vasculature, some epithelial cysts and interstitial cells. This is the first description of substantial in vivo gene transfer into both normal and cystic kidneys. The methodology could find application in the creation of new models of renal disease, for in vivo therapeutic intervention or for genetic modification of an allograft at the time of harvest.