Despite of the enormous knowledge accumulated about the genetic basis of human cancer, there have been only a few drugs which target the genetic differences between tumor cells and all normal cells in the body. To identify cancer-specific small molecules, a cell-based assay system which used co-culture strategy was newly developed. Co-culture of normal cells (WI38) and tumor cells (HCT-116) which expressed two different fluorescent proteins (YFP and CFP, respectively) allowed facile screening for cancer-specificity. Among 20,000 compounds screened, a novel compound, CGK3237, was identified that inhibited specifically the growth of HCT-116. Surprisingly, it was found out that only the growth of a certain type of cancer cells which had deregulated Wnt signaling pathway was selectively affected by CGK3237. By using a reporter assay for Wnt-dependent transcriptional activation, it was demonstrated that CGK3237 down-regulated the mRNA level of β -catenin and inhibited the occupancy of β-catenin onto TCF/LEF-responsive element. Consistent with this result, the activity of constitutively activated β-catenin in SW480 cells was also disturbed by CGK3237. The exact cellular target of CGK3237 was not identified yet, but these results suggest that chemical genomic approach is a very powerful method in searching for a novel anti-cancer drug.