Mucosal immune responses to pathogenic gut bacteria and the mechanisms that govern disease progression and outcome have been researched intensely for decades. More recently, the influence of the resident non-pathogenic or 'commensal' microflora on mucosal immune function and gut health has emerged as an area of scientific and clinical importance. Major differences occur in the mucosal immune response to pathogens and commensals. In part, this functional dichotomy is explained by the presence of virulence factors in pathogenic species, which are generally absent in commensals. Additionally, immunological 'unresponsiveness' towards the resident commensal microflora is thought to permit their successful colonisation and co-existence within the host gut. However, evidence of an active dialogue between members of the commensal microflora and the host mucosal immune system is rapidly unfolding. This crosstalk is likely to affect immunological tolerance and homeostasis within the gut and to explain some of the differential host responses to commensal and pathogenic bacteria.