 This study used intravital microscopy to observe the effects of in vivo blood flow on the decelularized glomerulus, peritubular capillaries, and tubules after autologous and allogeneic orthotopic transplantation into rats. The results showed that large molecular weight dextran molecules were able to label the vasculature, revealing substantial degrees of translocation from glomerular and peritubular capillary tracts to the decelularized tubular epithelium and lumen as early as 12 hours after transplantation. This process continued for up to one week, resulting in significant damage to the decelularized micro-architecture and thrombosis in both autologous and allogeneic approaches. These findings suggest that in vivo multifoton microscopy is a powerful tool for studying scaffold viability and identifying ways to promote scaffold longevity and vasculogenesis in bio-artificial organs. This article was authored by Peter R. Corridan.