Colorectal cancer (CRC) is a leading fatal carcinoma worldwide. Our goal was to investigate the effects of genistein on WNT signaling, which is involved in colon epithelial cell growth and apoptosis. Human colon cancer cell line DLD-1 was treated for four days with 75 μmol/L genistein. Decreased nuclear β-catenin and increased phospho-β-catenin accumulation was detected, showing a change in WNT signaling. Reverse transcriptase-polymerase chain reaction analysis showed increased sFRP2 (a WNT pathway antagonist) mRNA expression following the genistein treatment. Methylation selective polymerase chain reaction showed decreased methylation in two CpG islands of the sFRP2 gene following genistein treatment, similar to the effect of 5-aza-cytidine, a demethylation agent. We observed reduced DLD-1 cell viability and increased apoptosis with genistein treatment. Genistein inhibits β-catenin-mediated WNT signaling through increasing sFRP2 gene expression by demethylating its silenced promoter in colon cancer cell line DLD-1.