The colon of the simple-stomached animal comprises a gradually changing microbial environment, using the residues of digestion as substrates for fermentation. As carbohydrate sources decline along the length of the colon, the microflora degrade proteins to use as an energy supply, resulting in the formation of undesirable and potentially toxic metabolites. This study has examined the possibility of using dietary starches as a means of extending carbohydrate fermentation along the colon in order to reduce the effects of protein degradation, and the influence of these starches on the numbers of microbial groups within the total population. The study was carried out in weaned piglets, using native and retrograded forms of maize and waxy maize starches, containing proportionately about 0·25 and 0·01 amylose respectively. It was found that protein degradation in the mid and distal regions of the colon was best reduced by the inclusion of the retrograded form of waxy maize, although these data did not achieve significance. However, it was found that a reduced population of the protein-degrading Bacteroides spp. resulted from the inclusion of waxy maize rather than maize in the diets, (proximal colon P < 0·01 ; mid colon P < 0·001 , distal colon P < 0·05), while the retrograded waxy maize produced increased lactobacillixoliform ratios throughout the colon, which may result in an improved resistance to infection by intestinal pathogens. Retrogradation of these starches reduced the coliform populations throughout the colon, with significant (P < 0·05) effects observed in the proximal and distal regions. The data suggest that, of the starches tested, reduced protein-degrading activity and improved pathogen resistance may be achieved with retrograded waxy maize.