The number of preclinical and clinical studies showing efficacy of probiotics in the treatment and prophylaxis of certain diseases, e.g. diarrhoea of various origin, irritable bowel syndrome, inflammatory bowel disease, allergies, hypercholesterolemia, bacterial vaginosis, and colorectal cancer, is increasing. These health benefits are often species and strain specific. This article provides an overview of available knowledge about the supposed mechanisms of probiotic microorganisms action focusing in particular on the interaction between probiotic and host cells. One of the results of this interaction is induction of pro- or anti-inflammatory immune response in the macroorganism. Detailed knowledge of the signalling pathways involved in the communication between bacterial and human cells can find application in the selection of optimal probiotics for the targeted treatment of selected diseases. Additional possibilities for their use in clinical practice are provided by genetic manipulation of probiotic microorganisms.probiotics inflammation signalling pathways immunomodulation genetic manipulation.