Inflammatory diseases such as asthma and diabetes are rising in industrialized countries and the modern lifestyle that is associated with lower exposure to microbes has been held responsible for the increasing prevalence of these diseases. Several studies have shown an inverse association between pathogen-exposure and allergy or autoimmunity. The mechanisms behind such protective effects have been investigated at the epidemiological, cellular and molecular level and have provided data on the ability of lipids either derived directly from pathogens or up-regulated as a result of an infection to down-regulate immune responses and thereby control inflammatory diseases. In this mini-review, recent findings and new concepts relating to the immunosuppressive effects of endogenous lipids and those encountered upon exposure to bacteria, protozoa and particularly helminths are discussed. The overview focuses on the modulation of interactions between the antigen-presenting compartment and T cells to start an anti-inflammatory "program" with potential to regulate disease processes.