Procyanidins thus impact the composition and activity of intestinal microbiota by multiple mechanisms, however, data on the antimicrobial activity against most of the strict anaerobes of intestinal microbiota remains scarce and studies that directly compare antimicrobial and enzyme-inhibitory activity of procyanidins are scarce. The mechanisms of modulation of gut microbiota by procyanidins alone or in interaction with dietary fibre remain therefore largely unknown. It was therefore the aim of this study to directly compare the antimicrobial activity of procyanidins to the inhibition of digestive enzymes. Oligomeric procyanidins were extracted from grape seed extracts and separated by high-performance counter-current chromatography (HPCCC), an effective method for the fractionation of procyanidin-containing plant extracts. The fractionated monomeric and oligomeric flavan-3-ols were also used to determine the antimicrobial activity against a broad range of intestinal microorganisms, and the inhibition of rat digestive enzymes in vitro