FISH (fluorescent in situ hybridization) is a molecular cytogenetic technique established in the early 1980s that allows for the detection of DNA copy number changes (gains and losses) mapping to genomic regions of interest (Langer-Safer et al. Proc Natl Acad Sci USA 79:4381-4385, 1982). This technology has been extensively applied to research-based investigations and is routinely used in prenatal diagnosis and oncology. Here we describe a modification of the standard FISH protocol adapted for the detection of low-frequency mosaic aneuploidy in interphase cells. This approach represents a straightforward method for the measurement of aneuploidy levels in mammalian cells. This system combines four probes mapping to two different chromosomes. The choice of probes is essential for the successful performance of this approach. It greatly reduces the enumeration of false-positive signals that are challenging in the enumeration of ploidy changes (particularly if these are complex and/or involve a significant increase of chromosome number).