Bioinformatics analysis for Illumina Infinium Human DNA methylation BeadArray is essential, but still remains difficult task for many experimental researchers. We here aimed to develop a browser-accessible bioinformatics tool for analyzing the BeadArray data. The tool was established as an analytical pipeline using R, Perl and Python programming languages. We introduced a method that groups neighboring probes into a genomic block, which facilitated efficient identification of densely methylated/unmethylated regions. The tool, MACON, provided probe filtering, β-mixture quantile normalization, grouping into genomic blocks, annotation and production of a data subset. MACON allows researchers to analyze the BeadArray data using a web browser (http://epigenome.ncc.go.jp/macon).