Background Gene expression studies on the effect of hypoxia and hyperglycemia using human umbilical vein endothelial cell (HUVEC) cultures are of particular interest in cardiovascular disease and diabetes. Normalization of gene expression data refers to the comparison of expression values using endogenous control that is steady across independent experimental conditions, a crucial step for gene expression studies. The endogenous controls for experiments involving hyperglycemia, hypoxia and a combination of the two have not been identified before in HUVEC. Our objective was to identify endogenous controls that are stable under oxidative (hypoxia) and metabolic stress (hyperglycemia) in HUVEC.