The use of endothelial progenitor cells (EPCs) is a promising new treatment option for cardiovascular diseases. Many of the underlying mechanisms that result in an improvement of endothelial function in vivo remain poorly elucidated to this date, however. We summarize the current positions and potential applications of gene-expression profiling in the field of EPC biology. Based on our own and published gene-expression data, we demonstrate that gene-expression profiling can efficiently be used to characterize different EPC types. Furthermore, we highlight the potential of gene-expression profiling for the analysis of changes that EPCs undergo during culture and examine changes in gene transcription in diseased patients. Transcriptome profiling is a powerful tool for the characterization and functional analysis of EPCs in health and disease.