Experimental autoimmune encephalomyelitis (EAE) is mediated by myelin-specific CD4+ T cells secreting Th1 and/or Th17 cytokines. Signal transducer and activator of transcription (STAT) family proteins have essential roles in transmitting Th1 and/or Th17 cytokine-mediated signals. However, most studies demonstrating the importance of the STAT signaling system in EAE have focused on distinct members of this family, often looking at their role specifically in the central nervous system, or in vitro. There is limited information available regarding the temporal and spatial expression patterns of each STAT protein and interplay between STAT proteins over the course of EAE development in critical lymphatic organs in vivo. In the present study, we demonstrate dramatic and progressive decrease of all six STAT family members (STAT1, STAT2, STAT3, STAT4, STAT5, STAT6) in the spleen and lymph nodes through the course of EAE development in SJL/J mice, in contrast with almost steady expression of thymic STAT proteins. Decreased splenic and lymphatic STAT expression was accompanied by significant enlargement of the spleen and lymph nodes, and histological proliferation of T cell areas with remodeling of the splenic microstructure in EAE mice. All STAT family members except STAT2 were mainly confined in T cell areas in spleen, whereas they were distributed in a protein specific manner in thymus. We present here a comprehensive analysis of all six members of the STAT family in spleen, lymph nodes and thymus through the development phase of EAE. Results suggest that EAE induced inflammatory T cells may develop distinct biological features different from normal splenic T cells due to altered STAT signaling.