The location and level of DNA methylation within a genome is emerging as an important biomarker for cancer diagnosis. Despite its potential, it is difficult to comprehensively analyze the epialleles that are often found in a biological sample. Therefore, an assay utilizing molecular inversion probes was designed and used to expose and quantify epialleles in heterogeneously methylated bisulphite treated genomic DNA. Different CpG dinucleotides were able to be rapidly quantified with high resolution, sensitivity and specificity over a large dynamic range using rapid flow cytometric readout of multiplexable microbead DNA biosensors.