Degradation of a sample of high-molecular (degree of polymerisation, DP, between 13 and 30) and low-molecular (DP below 12) inulin from Jerusalem artichoke during dry heating for 30 min at 165 and 195 °C was analysed using high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and thin layer chromatography. Dry heating at 195 °C induced complete degradation of the fructan chains and the concomitant formation of low-molecular degradation products, most likely di-d-fructose dianhydrides. In vitro fermentation studies using mixed faecal samples of eight human volunteers for 24 h at 37 °C showed significant stimulation of the growth of bifidobacteria and Enterobacteriaceae and a significant decrease of possibly pathogenic bacteria of the Clostridium histolyticum and C. lituseburense group by inulin samples heated at 195 °C compared to unheated samples and samples heated at 165 °C. This preliminary data may point to the hypothesis that heat-treated inulin or its degradation products may cause improvements of the gut microflora superior to native inulin.