DNA methylation in human genome is important for the cells specialization and functioning. An abnormal methylation of the regulation regions of some genes may cause the genes silencing and this phenomenon is often detected in cancer cells. Determination of differences of the genome-wide methylation in normal and tumor cells is useful for understanding the carcinogenesis process and for development of new methods of epigenetic diagnostics. The positions of methylated RCGY sites in the genomes of Raji, U-937 and L68 human cell lines have been determined using the previously developed method of massive parallel sequencing of Glal fragments. A comparison of the obtained data has revealed significant differences in methylation of CpG islands, putative regulatory regions and some repetitive DNA families between genomes of malignant and non-malignant cells. GO enrichment analysis of genes with highly methylated regulatory regions has shown the possible metabolic processes, which may be affected epigenetically in carcinogenesis. The new method allows to determine positions of many modified cytosine bases in the genomes and may be a simple alternative to the existing methods of genome-wide methylation analysis.