Background: SALL4 is a critical transcription factor for stem cell character maintenance. Results: SALL4 protein interacts with different DNA methyltransferases and associates with enzymatic activities. Overexpression of SALL4 induced increased DNA methylation in promoter regions of silenced genes. Conclusion: SALL4 may form a large complex with epigenetic modifiers in suppressing gene expression. Significance: A novel mechanism is provided by which stem gene SALL4 negatively regulates target genes.