The aim was to study the effect of physical processes (autoclaving/cooling cycles and spray drying) on starches having different crystalline structure: wheat (type A) or potato (type B) starch. First, the extent of changes in the physico-chemical properties of these physically-modified starches as the carbon and energy sources for growth in in vitro conditions was investigated. Characteristics of functional properties, e.g. water binding capacity (WBC), indicated that both native starches had low affinity to water, that increased however 4-times after modification. The opposite tendency was observed for fat absorption (FA). Viscosity of water dispersion dramatically decreased after modification of both starches. The ability of the tested Bifidobacterium strains to metabolise native or physically- modified wheat and potato starches was differentiated. B. pseudolongum KSI9 and B. animalis KSD29a3 isolated from animals utilised the examined starches as easily accessible substrates of fermentation, whereas B. breve ATCC 15700 isolated from human did not metabolise or only negligibly fermented starch preparations. The number of bifidobacteria populations as well as their acidifying activity were higher in the media containing wheat starch in comparison to the potato starch, whereas no significant differentiation was observed between the results obtained in media with native or modified starch. The results suggest that native or experimentally-modified wheat and potato starches with some fraction of resistant starch can be a good substrate for colonic bifidobacteria.