The hygiene hypothesis proposes that the stimulation of the immune system by microbes or microbial products protects from the development of inflammatory diseases; therefore a reduced exposure to infectious agents may explain the rise in allergic and autoimmune diseases in industrialized countries. The contribution of studies on parasites and allergy to our understanding of the hygiene hypothesis has been two-fold. First, several studies have shown an inverse association between exposure to (Toxplasma gondii) or harbouring of parasites (Schistosoma or Intestinal helminths) and allergy. Second, the mechanisms behind such protective effects have provided new insights and theories on the ability of parasite derived molecules to down-regulate immune responses and thereby to control inflammatory diseases such as allergies. In this review, recent findings and new concepts relating to the associations between parasites and allergies at the epidemiological, cellular and molecular level are discussed.