The objective of this project was to analyze the first thymic alterations during the course of experimental autoimmune encephalomyelitis (EAE). Our data has shown that during the development of EAE, thymus presented a relative size reduction, loss of cortico-medullary delimitation and alterations in the proportion of thymocytes. Such results suggest an alteration in the stromal compartment of thymic microenvironment and in the selection and development of T cells.