The thymus is a primary lymphoid organ that plays an important role in the development of the immune system and in the differentiation and maturation of the vast majority of the T cell repertoire. During the normal life span, this organ undergoes involution in situations such as pregnancy, aging and in the presence of a wide variety of infectious diseases. This atrophy is characterized by intense structural and morphological alterations associated with an increased level of apoptosis, for which many direct and indirect mechanisms have been proposed. The fact that the thymus is a target for infectious diseases could make the host environment propitious for the maintenance or enhancement of infection.