International audience A central question for immunology is: what does the immune system recognize andaccording to which principles does this kind of recognition work? Immunology has beendominated by the idea of recognizing molecular structures and triggering an appropriateimmune response when facing non-self or danger. Recently, characterizations in termsof function have turned out to be more conserved and explanatory in microbiota researchthan taxonomic composition for understanding microbiota-host interactions. Startingfrom a conceptual analysis of the notions of structure and function, I raise the titlequestion whether it is possible for the immune system to recognize microbial functions.I argue that this is indeed the case, making the claim that some function-associatedmolecular patterns are not indicative of the presence of certain taxa (“who is there”) butof biochemical activities and effects (“what is going on”). In addition, I discuss casestudies which show that there are immunological sensors that can directly detectmicrobial activities, irrespective of their specific structural manifestation. At the sametime, the discussed account puts the causal role notions of function on a more realist andobjective basis.