Human umbilical vein endothelial cell (HUVEC)-based gene expression studies carried out under hypoxia and/ or hyperglycemia bear huge potential in modelling endothelial cell response in cardiovascular disease and diabetes. However, such studies require reference genes that are stable across the whole range of experimental conditions. These reference genes have not been comprehensively defined to date. We applied human genome-wide microarrays and quantitative real-time PCR (qRT-PCR) on RNA obtained from primary HUVEC cultures that were incubated for 24 h either in euglycemic or hyperglycemic conditions and then subjected to short-term CoCl2-induced hypoxia of either 1, 3 or 12 h. Using whole-transcript arrays, we selected ten commonly used reference genes with no significant expression variation across 8 different conditions. These genes were ranked using NormFinder software according to their stability values. Consequently, five genes were selected for validation by quantitative real-time PCR (qRT-PCR). These were: ribosomal protein large P0 (RPLP0), transferrin receptor (TFRC), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-glucuronidase (GUSB), and β-actin (ACTB). All five genes displayed stable expression under hyperglycemia. However, only RPLP0 and TFRC genes were stable under hypoxia up to 12 h. Under hyperglycemia combined with hypoxia up to 12 hours the expression of RPLP0, TFRC, GUSB and ACTB genes remained unchanged. Our findings strongly confirm that RPLP0 and TFRC are the most suitable reference genes for HUVEC gene expression experiments subjected to hypoxia and/or hyperglycemia for the given experimental conditions. We provide further evidence that even commonly known references genes require experimental validation for all conditions involved.