Abstract: Provided is a method for determining genomic imprinting disorders in a patient based upon methylation specific primer extension in a format amenable to high throughput and multiplex formats. After bisulfite modification of a genomic sample, DNA is amplified and hybridized to discrimination primers specific for a CpG dinucleotide site in the sample. Because no extension products from the discrimination primers are produced from DNA that has a deletion or functional inactivation at the CpG site, the sample may be diagnosed as having a genomic imprinting disorder by way of comparison with a normal sample.