Signal regulatory protein (SIRP), also known as SHPS-1/SIRPA, is an immunoglobulin superfamily protein that binds to the protein tyrosine phosphatases Shp1 and Shp2 through its cytoplasmic region and is predominantly expressed in dendritic cells and macrophages. CD47, a widely expressed transmembrane protein, is a ligand for SIRP, with the two proteins constituting a cell-cell communication system. It was previously demonstrated that the CD47-SIRP signaling pathway is important for prevention of clearance by splenic macrophages of red blood cells or platelets from the bloodstream. In addition, this signaling pathway is also implicated in homeostatic regulation of dendritic cells and development of autoimmunity. Here we describe the detailed protocols for methods that were used in our recent studies to study the role of the CD47-SIRP signaling pathway in autoimmunity. We also demonstrate that hematopoietic SIRP as well as nonhematopoietic CD47 are important for development of experimental autoimmune encephalomyelitis. Thus, we here strengthen the importance of experimental animal models as well as other methods for the study of molecular pathogenesis of autoimmunity.