The present invention provides rapid and inexpensive methods for determining the copy number of a test locus of interest. The methods generally involve monitoring the formation of amplification product using real time amplification detection systems to quantify the amount of test locus and reference loci in a test subject and the amount of test locus and reference loci in at least one control subject. The methods can be used to interrogate the copy number of loci containing simple sequence repeats. Since such sequences are ubiquitous in eukaryotic genomes, the present methods have wide-ranging applicability. The methods of the present invention can be used as diagnostic and prognostic tools and in correlating abnormal copy number values for specific loci with disease and effectiveness of different treatment options.