The antimicrobial activity of saponins from Medicago sativa, M. arborea and M. arabica against a selection of medically important yeasts, Gram-positive and -negative bacteria was investigated. Structure-activity growth inhibitory effects of related prosapogenins and sapogenins are also described. Increasing antibiotic activity was observed going from the saponin extracts to the sapogenin samples, suggesting that the sugar moiety is not important for the antimicrobial efficacy. Activity was especially high against Gram-positive bacteria (Bacillus cereus, B. subtilis, Staphylococcus aureus and Enterococcus faecalis) with M. arabica being the species showing a broader spectrum of action. Discrete antifungal activity was also observed, mainly against Saccharomyces cerevisiae. The observed antimicrobial properties of M. sativa and M. arborea were related to the content of medicagenic acid, while hederagenin seems to contribute to the bioactivity of M. arabica total sapogenins.