It was examined whether the physiological effects of high-amylose maize starch (HAMS) are influenced by hydroxypropylation. Rats were fed one of the following three diets: an AIN-93-based diet with waxy maize starch (WMS) as a starch source, or this diet with 150 g of WMS replaced by either HAMS or hydroxypropylated HAMS (HP-HAMS). The activities of amylase in bile-pancreatic juice and sucrose, maltase and isomaltase of the jejunum and ileum were not affected by diet, but the digestibility of HAMS was decreased by hydroxypropylation. The amounts of SCFA in caecal content and H2 excreted in the breath and flatus for HAMS were decreased by hydroxypropylation. Plasma glucagon-like peptide-1 (GLP-1), glucose and insulin concentrations were not affected by diet. On the basis of PCR-denaturing gradient gel electrophoresis (DGGE) profiles, the similarity in caecal bacteria population of the HP-HAMS group and HAMS group was low, but that of the HP-HAMS and WMS groups was high. The amount of caecal IgA was not affected by hydroxypropylation, but those in the HAMS and HP-HAMS groups were greater than that in the WMS group. Plasma and liver concentrations of TAG and cholesterol for HAMS were not affected by hydroxypropylation. These results show that the small intestinal digestibility and fermentation-dependent parameters such as caecal SCFA and H2 productions and caecal bacterial profile of HAMS were affected by hydroxypropylation, but parameters of glucose metabolism such as GLP-1 and insulin, those of lipid metabolism such as plasma TAG and cholesterol and the amount of caecal IgA were not.