An in vitro method of quantifying methylation of one or more genes of interest (TARGETgene) in a sample from a subject and/or diagnosing development of a disease associated with aberrant DNA methylation comprising: a) adding to the sample containing DNA from the subject, a plurality of copies of a STDgene specific for each TARGETgene of interest being detected; wherein each STDgene DNA is designed with 5' and 3' regions identical to a TARGETgene of interest, and the number of intervening bases between the 5' and 3' regions in the STDgene is essentially the same as the region of interest within the TARGETgene, b) isolating and processing the DNA in the sample; c) preparing the DNA in (a) for methylation specific PCR; d) amplifying the DNA in (b) with one or more pairs of external methylation-independent PCR primers, where each single primer pair is capable of selectively hybridizing to only one TARGETgene of interest being detected and the STDgene specific for that TARGETgene, using PCR under conditions sufficient to produce a first amplification product; e) obtaining a diluted sample of the first amplification product of (d); f) adding to (e) one pair of internal methylation-dependent PCR primers specific for each TARGETgene of interest, and one pair of internal PCR primers specific for the STDgene for the TARGETgene of interest, one or more optically detectable labeled DNA probes which specifically hybridize to each TARGETgene of interest, and one or more optically detectable labeled DNA probes which specifically hybridize to each STDgene for the TARGETgene of interest; and g) amplifying the DNA in (f) using quantitative real-time PCR under conditions sufficient to produce a second amplification product which provides quantification of the amount of copies of the methylated TARGETgene of interest and the amount of copies of the STDgene for the TARGETgene of interest. a) adding to the sample containing DNA from the subject, a plurality of copies of a STDgene specific for each TARGETgene of interest being detected; wherein each STDgene DNA is designed with 5' and 3' regions identical to a TARGETgene of interest, and the number of intervening bases between the 5' and 3' regions in the STDgene is essentially the same as the region of interest within the TARGETgene, b) isolating and processing the DNA in the sample; c) preparing the DNA in (a) for methylation specific PCR; d) amplifying the DNA in (b) with one or more pairs of external methylation-independent PCR primers, where each single primer pair is capable of selectively hybridizing to only one TARGETgene of interest being detected and the STDgene specific for that TARGETgene, using PCR under conditions sufficient to produce a first amplification product; e) obtaining a diluted sample of the first amplification product of (d); f) adding to (e) one pair of internal methylation-dependent PCR primers specific for each TARGETgene of interest, and one pair of internal PCR primers specific for the STDgene for the TARGETgene of interest, one or more optically detectable labeled DNA probes which specifically hybridize to each TARGETgene of interest, and one or more optically detectable labeled DNA probes which specifically hybridize to each STDgene for the TARGETgene of interest; and g) amplifying the DNA in (f) using quantitative real-time PCR under conditions sufficient to produce a second amplification product which provides quantification of the amount of copies of the methylated TARGETgene of interest and the amount of copies of the STDgene for the TARGETgene of interest.