Prolonged culture of pluripotent and multipotent stem cells exposes the cells to strong selection pressures, often resulting in genomic alterations. Any genetic manipulation of the cells may further jeopardize their genomic stability. Genomic aberrations affect the differentiation capacity of stem cells, their stem cell identity and their tumorigenicity, and should thus be routinely evaluated for their proper use in basic research and in clinical trials. Here we review the common methods currently available to analyze the genomic integrity of stem cells, and present a recently developed method for the evaluation of the genomic integrity of stem cells by their gene expression profiles. We describe the principles of this method, provide guidelines for its implementation, and discuss its advantages and limitations compared to other available methods.