Interest is increasing in the transplantation of pancreatic islets as a means to achieve insulin independence in individuals with type I diabetes. The success of this approach is hampered by the absence of methods to follow the fate of transplanted islets non-invasively. In vivo imaging seems to be the most appropriate technique to achieve this goal in small animals and eventually in humans. Here we describe a protocol for labeling and subsequent imaging of transplanted islets in vivo using magnetic resonance imaging (MRI) and optical imaging. The whole series of experiments can be carried out in roughly 48 h. We believe that our approach can significantly advance the current ability to determine islet distribution, and possibly survival, after transplantation. This information would be essential not only for the long-term monitoring of graft function but also for the design of improved transplantation and immunomodulatory methods.