Interest in probiotic bacteria, in the context of health and disease, is increasing and gathering scientific evidence, as is reflected by their growing utilization in food and pharma industry. As a consequence, many research effort over the past few years has been dedicated to discern the molecular mechanisms responsible for their purported attributes. Remarkably, whereas the traditional probiotic concept assumes that bacteria must be alive during their administration to exert health-promoting effects, evidence is being accumulated that supports defined bacterial secreted molecules and/or isolated surface components mediating attributed cross talk dialogue between the host and the probiotic cells. Indeed, administration of the isolated bacterial-derived metabolites or molecules may be sufficient to promote the desired effects and may represent a promising safer alternative in inflammatory disorders. Here, we summarize the current knowledge of molecular effectors of probiotic bacteria that have been involved in mediating their effects.