The gut microbiota continues to fascinate scientists in many realms when it is considered that humans contain 90% bacteria. Correlations between changes in composition and activity of the gut microbiota and common disorders such as cancer, hypertension, hypercholesterolemia, inflammatory bowel diseases, obesity, oral health, etc. have been proposed. What is the real role of probiotics, prebiotics and synbiotics in influencing a healthy microbiota? Both in vitro evidences and in vivo clinical data have supported some of these new health claims, while recent molecular advancement has provided strong indications to support and justify the hypotheses. However, probiotics validity and health claims have continuously been rejected on the basis of “biomarker deficiency”. To battle the increase in health care costs, a preventive approach to medicine with the development of probiotics and prebiotics or symbiotic products is being advanced. This review discusses the potential beneficial effects of probiotics in preventing and treating certain diseases as well as current and future perspectives of probiotic research.