The present invention relates to a method for the quantitative analysis of methyl cytosine in a gene. The method comprises the steps of: (1) treating genomic DNA extracted from a cell or tissue sample with bisulfite so as to maintain methyl cytosine intact and to convert unmethylated cytosine into uracil; (2) selectively amplifying a target gene by PCR using the DNA treated in said step (1) as a template in a reaction mixture containing primers specific for the target gene, dNTP and polymerase; (3) removing non-specific amplification products, the dNTP and the primers from the product amplified in said step (2) to purify the target gene; (4) cleaving the target gene purified in said step (3) into a deoxynucleotide monophosphate (dNMP) level; and (5) separating the dNMP-level product cleaved in said step (4) using capillary electrophoresis, to thereby quantify and measure the content of the methyl cytosine in the target gene. Also, the present invention provides a method for classifying or diagnosing aging, cancer, pathogens, pathogenic contamination, tissues and individuals in a sample, the method comprising measuring the content of methyl cytosine in the sample using the quantitative analysis method of methyl cytosine, and comparing the measured content with the database content of methyl cytosine for aging, cancer, pathogens, tissues or individuals. The inventive method for the quantitative analysis of DNA methylation enables the degree of DNA methylation to be quantified in a highspeed, high-sensitivity and automatable platform, which has not yet been achieved by any of the prior methods.