Ligand-dependent activation of the Hedgehog (Hh) pathway in colorectal cancers (CRCs) is controversial, and the regulation mechanism of Hh ligands expression remains to be determined. In the present study, the mRNA expressions of Sonic hedgehog (SHH), Indian hedgehog (IHH), Patched, Smoothened, and Gli1 were examined in four cultured colon cancer cell lines by reverse transcription-PCR. Moreover, ligands mRNA expression (SHH and IHH) were examined by reverse transcription-PCR, and SHH protein expression by immunohistochemistry in 25 primary CRCs. The methylation status of SHH and IHH was also investigated by bisulfate sequencing or methylation specific PCR. IHH mRNA was completely absent in cell lines studied, and expressed at a very low level or not expressed at all in primary CRCs. Methylation analysis revealed that IHH promoter was hypermethylated in colon cancer cell lines. Absence of SHH mRNA expression and hypermethylation of its promoter was also observed in colon cancer cell lines. However, high level expression of SHH and hypomethylation of its promoter was detected in primary CRCs. In conclusion, ligand dependent activity of Hh pathway is inactive in cultured colon cancer cells correlating to ligands hypermethylation. In contrast, SHH overexpression, possible consequence of promoter hypomethylation, could play a role in the carcinogenesis of primary CRCs.