The discovery of peripheral circulating cells that contribute to vasculogenesis and endothelial repair was one of the most fascinating breakthroughs in the domain of vascular research during the last two decades. The population of vasculogenic cells however, is heterogeneous and can be analyzed using different approaches including in vitro culture and flow cytometry. Circulating CD34(+)/KDR(+)/CD45(dim) endothelial progenitor cells (EPC) have a great potential as biomarkers in various cardiovascular diseases. With the expanding interest in this field, the development of standardized protocols is critical. In this review we describe in detail the pre-analytical and analytical factors that should be taken into account when quantifying CD34(+)/KDR(+)/CD45(dim) EPC using flow cytometry. Moreover, technical suggestions in order to enhance accuracy and reproducibility of this enumeration are provided.