Lactulose is used as a triggering substance in a unique colon-specific delivery technology called CODESTM. Colonic microflora degrades lactulose and forms short-chain fatty acids to activate the CODESTM system. However, lactulose has been reported to cause a Maillard-type reaction with substances containing primary or secondary amino groups that may produce carcinogenic compounds. Thus, the aim of this study was to look into the possibility to substitute lactulose with isomalt for fabrication of CODESTM. The in vitro degradation of both sugars before incorporating them into the CODESTM system was evaluated with the help of rat caecal microflora. The results showed that isomalt was less efficient with regard to its rate and extent of degradation into short-chain fatty acids by the microflora compared to lactulose. However, the in vitro dissolution study did not show a significant difference in the performance between lactulose and isomalt when they were incorporated separately in CODESTM. A similar result was also obtained in the in vivo study. Based on the above results, isomalt could be used as an alternative to lactulose for colonic delivery system utilizing the principles of CODESTM.