Dietary resistant starch (RS), as a high amylose maize starch (HAMS), prevents dietary protein-induced colonocyte genetic damage in rats, possibly through the short-chain fatty acid (SCFA) butyrate produced by large bowel bacterial RS fermentation. Increasing butyrate availability may improve colonic health and dietary high amylose maize butyrylated starch (HAMSB) is an effective method of achieving this goal. In this study, rats (n = 8 per group) were fed diets containing high levels (25%) of dietary protein as casein with 10 or 20% dietary HAMSB and HAMS. Colonocyte genetic damage was measured by the comet assay and was 2-fold higher in rats fed 25% protein than those fed 15% protein (P < 0.001). Concurrent feeding of 25% protein and either HAMS or HAMSB lowered genetic damage significantly relative to a low-RS high-protein control diet. The 20% HAMSB diet was twice as effective as 20% HAMS in opposing genetic damage. Large bowel digesta butyrate was significantly increased in rats fed 20% compared with 10% HAMS and in rats fed 20% compared with 10% HAMSB. The levels were significantly higher in the HAMSB groups relative to the HAMS groups. Hepatic portal venous SCFA were higher in rats fed HAMS and highest in those fed HAMSB. Caecal digesta ammonia was increased by HAMSB and correlated negatively with digesta pH. Ammonia is cytotoxic and lower digesta pH could lower its absorption, possibly contributing to lower genetic damage. Delivery of butyrate to the large bowel by HAMSB could reduce colorectal cancer risk by preventing diet-induced colonocyte genetic damage.