Autoimmune diseases are characterized by infiltration of the target tissue with specific immune cells that ultimately leads to the destruction of normal tissue and the associated disease. There is a need for imaging tools that allow the monitoring of ongoing inflammatory disease as well as the response to therapy. We discuss new magnetic resonance imaging-based technologies that have been used to monitor inflammation and disease progression in animal models of type 1 diabetes, multiple sclerosis, and rheumatoid arthritis. Therapeutic strategies for these diseases include the transfer of immune cells, such as dendritic cells, with the aim of preventing or halting the disease course. We discuss several new MRI labeling techniques developed to allow tracking of immune cells in vivo. These include direct ex vivo labeling techniques as well as the genetic modification of cells to allow them to produce their own contrast agents. This is an area of intense recent research and can be expanded to other conditions such as cancer.