A large number of experimental and clinical studies published in recent years have demonstrated the beneficial role of probiotic bacteria in the health of the host. However, because the different receptors of the innate immune system can recognize only specific bacterial molecular patterns, knowledge of the role played by individual probiotic molecular patterns is essential to move from the current confused era of live probiotic bacteria to the era of the pharmacobiotic strategies. This article reviews the current knowledge on the probiotic activities of bacterial structural molecules (nucleic acids and surface molecules), which represent the fundamental basis to set up experimental and clinical studies in this emerging field with very promising and potentially invaluable future prospects.