Intravital imaging approaches are proving to be essential to address new questions to better understand how the immune system operates. These approaches are especially valuable to characterize the complex organization of immune responses in vivo. Here, we examine how to take advantage of the cornea as a natural body window to apply noninvasive imaging techniques to assess cytotoxic T lymphocyte involvement in the immune rejection process in a model of intraocular allogeneic islet transplantation.