Recently, with the acetylation of histone and the modification of chromatin structure, the methylation of cytosine residue within CpG dinucleotides in genomic DNA sequence attracts many researchers' attention as one of major epigenetic regulation systems of gene expression. There are several methods (immunofluorescence with 5-methylcytosine specific antibody and methylation-sensitive restriction enzyme-PCR method, etc.) to analyze the methylation of cytosine residue. Bisulfite-sequencing method, which is one of methods for analyzing the methylation of cytosine residue in genomic DNA sequence, has advantages of high sensitivity and analyzing the methylation of cytosine residue directly. In this note, the detailed procedure of bisulfite-sequencing method for mouse early pre-implantation embryos is described.