The effects of resveratrol and pterostilbene (two structurally related stilbene compounds) on three human colon cancer cells were systematically compared. Cell viability tests indicated that IC(50) values of pterostilbene were 2-5-fold lower than those of resveratrol in all three cancer cells. Pterostilbene was also more potent in inhibiting colony formation of all three cancer cells. Annexin V/propidium iodide costaining assay and Western blotting analysis showed pterostilbene had a stronger apoptosis-inducing effect, which was evidenced by the higher percentage of annexin V positive cells and higher levels of cleaved caspase-3 and poly(ADP-ribose) polymerase proteins in cancer cells treated with pterostilbene compared with resveratrol. High-performance liquid chromatography analysis demonstrated that intracellular levels of pterostilbene were 2-4-fold higher than those of resveratrol after treatments with individual compounds at the same concentration. Overall, the results demonstrated that pterostilbene had more potent inhibitory effects on colon cancer cells than resveratrol, which may be associated with the superior bioavailability of pterostilbene to resveratrol.