The physical and chemical properties of commercial low methoxyl citrus pectins, CP 28 and CP 55, and a pectinmethylesterase (PME) charge modified citrus pectin (MP 38) were compared, and the differences in ability to encapsulate indomethacin in hydrogel beads was determined at 0.5 or 1.0% (w/v) indomethacin ratio, and 100, 200 or 300 mM CaCl(2) solution. In order to investigate the drug release characteristics, indomethacin loaded dried hydrogel beads were immersed in simulated gastric fluids (pH 1.2) for 2h, followed by immersing in simulated intestinal fluids (pH 7.4) for 3h. Pectin type was highly significant (p<0.0001) for encapsulation efficiency and in vitro release assay. Encapsulation efficiency was also highly affected (p<0.0001) by indomethacin ratio and CaCl(2) concentration. The accumulative release rate of indomethacin from pectin hydrogel bead was less than 15% in simulated gastro-intestinal fluids. MP 38 beads showed significantly higher entrapment efficiency and lower release rate than beads formed from CP 28 or CP 55. MP 38 hydrogel formulated with 300 mM CaCl(2) and 0.5% indomethacin ratio showed the highest entrapment efficiency. These studies suggest that charge modification of pectin improves encapsulation efficiency of drugs for colon targeted drug delivery system through oral administration.