Several hundred species of bacteria inhabit the gut, and affect its cell biology, morphology and homeostasis. Many bacteria are however potential pathogens, especially if the integrity of the epithelial barrier is physically or functionally breached. Conversely, the interaction between host and commensal microbes can confer important health benefits. This has led to commercial and public interest in ’probiotics’, live microbes principally taken as food supplements. Might probiotics also be used in disease therapy? Experimental evidence that probiotics modulate gut physiology, particularly barrier integrity and immunological function, underpins exciting new gastroenterological research. We discuss below the scienti?c basis for probiotic effects and present a critical perspective for their use in relation to gastrointestinal disease. Several hundred species of bacteria inhabit the gut, and affect its cell biology, morphology and homeostasis. Many bacteria are however potential pathogens, especially if the integrity of the epithelial barrier is physically or functionally breached. Conversely, the interaction between host and commensal microbes can This has led to commercial and public interest in ’probiotics’, live microbes principally taken as food supplements. Might probiotics also be used in disease therapy? Experimental evidence that probiotics modulate gut physiology, particularly barrier integrity and immunological function, underpins exciting new gastroenterological research. We discuss below the scienti? c basis for probiotic effects and present a critical perspective for their use in relation to gastrointestinal disease.