Pectin is an important dietary component of all fruits and vegetables. Some pectins have been shown to inhibit cancer cell growth, but the effective structures and mechanisms have remained unclear. In this study, we investigated the effects of four structurally distinct pectins on human colon cancer HT-29 cells and the possible mechanisms accounting for the actions. The proliferation inhibitory effect was examined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Flow cytometry was used to visualize the cell cycle distribution. An reverse transcription polymerase chain reaction (RT-PCR)-based assay was utilized to detect mRNA levels of the proteins related to cell cycle arrest. The data showed that the rhamnogalacturonan I domain-rich pectin from potato inhibited the proliferation of HT-29 cells and induced significant G2/M cell cycle arrest. This inhibitory effect was due to the down-regulation of cyclin B1 and cyclin-dependent kinase 1 expression, but not p21(WAF1/CIP1) expression. The results suggested that the rhamnogalacturonan I domain might relate to the anticancer activity of pectin.