The present study aimed to investigate the anticancer effect of aloe-emodin, an anthraquinone compound present in the leaves of Aloe vera, on two human colon carcinoma cell lines, DLD-1 and WiDr. Colon carcinoma cells were treated with various concentrations of aloe-emodin for different durations. Cell viability was measured by sodium 3'-[1-(phenylamino-carbonyl)-3,4-tetrazolium]-bis(4-methoxy-6-nitro) benzene-sulfonic acid hydrate assay. DNA fragmentation was analyzed by agarose gel electrophoresis. Nuclear shrinkage was visualized by Hoechst 33258 staining. Western blotting was used to indicate the release of apoptosis-inducing factor and cytochrome c from mitochondria and the phosphorylation of Bid. Caspase-3 and casein kinase II activities were measured by the respective assays. Cell viability analyses showed that aloe-emodin induced cell death in a dose- and time-dependent manner. Notably, the WiDr cells were more sensitive to aloe-emodin than the DLD-1 cells. Aloe-emodin caused the release of apoptosis-inducing factor and cytochrome c from mitochondria, followed by activation of caspase-3 leading to DNA fragmentation, nuclear shrinkage and apoptosis. In addition, exposure of colon carcinoma cells to aloe-emodin suppressed the casein kinase II activity in a time-dependent manner and was accompanied by a reduced phosphorylation of Bid, a downstream substrate of casein kinase II and a pro-apoptotic molecule. These findings showed that the inhibition of casein kinase II activity, the release of apoptosis-inducing factor and cytochrome c, and the caspase-3 activation are involved in aloe-emodin-mediated apoptosis in colon carcinoma cells.