The cytogenetic analysis of single cells, such as oocytes and polar bodies, is extremely challenging. The main problem is low probability of obtaining a metaphase preparation in which all of the chromosomes are sufficiently well spread to permit accurate analysis (no overlapping chromosomes, no chromosomes lost). As a result, a high proportion of the oocytes subjected to cytogenetic analysis are not suitable for traditional chromosome banding studies or for molecular cytogenetic methods such as spectral karyotyping (SKY) or multiplex fluorescence in situ hybridization (M-FISH). Fortunately, recent innovations in whole genome amplification and microarray technologies have provided a means to analyze the copy number of every chromosome in single cells with high accuracy. Here we describe the use of such methods for the investigation of chromosome and chromatid abnormalities in human oocytes and polar bodies.