Probiotics are living microorganisms that, when administered in adequate amounts, confer health benefits on the host. Because probiotics are not marketed as pharmaceuticals, they are commercially available without rigorous scientific documentation of their efficacy for many health-related claims. Results from existing clinical trials are both confusing and controversial. The evidence base is relatively limited, includes studies with varied designs, assesses multiple probiotic preparations across discrepant disease states, and provides conflicting results. Recent advances in the delineation of probiotics' mechanisms of action offer the opportunity to construct a more logical framework within which future trials are designed.