Digital PCR enables the high precision, absolute quantification of nucleic acid target sequences through volumetrically defined partitioning. This precision, coupled with the removal of PCR efficiency biases and the need for a standard curve, has instituted its widespread adoption over other quantitative methods. Digital PCR is particularly well suited for precise copy counting of chromosome numbers in cells, making it a viable alternative to traditional karyotyping in many instances. Here we describe a multicolor multiplex digital PCR method of screening ES cell clones for aneuploidy for cheaper and swifter validation. This method can also be easily applied to other in vitro cellular models that require accurate analysis for copy number variations.