Several studies confirm a protection of cardiovascular diseases and certain forms of cancer by dietary flavonoid intake. The bioavailability of flavonoids is influenced by the metabolism of the microflora in the intestine. Using a new in vitro model system the deglycosylation of the flavonol rutin and the degradation of its aglycone quercetin were investigated by using fresh pig caecal inocula in comparison to inocula prepared before by freeze-preservation between 6 wk and 5 months. The incubation experiments led to the same pattern of phenolic degradation products in comparable amounts in both preparations using HPLC-DAD and GC-flame ionization detection (GC-FID) or GC-MS detection within 24–48 h of incubation. With the preservation of the microbial vitality and the metabolic efficiency by freeze-preparation over several months the experimental design of microbial metabolism studies will be independent in time and locality.