Transplantation involves preoperative ischemic periods that contribute to endothelial cell (EC) dysfunction and T-cell activation, leading to graft rejection. As hypoxia is a major constituent of ischemia, we evaluated its effect on the ability of ECs to express HLA-DR, which is required for presentation of antigens to T cells, and by itself serves as an important target for allogeneic T cells. Primary human umbilical vein ECs (HUVEC) and the human endothelial cell line EaHy926 were incubated in normoxia or hypoxia (PO2 < 0.3%). Hypoxia increased the membranal expression (by 4–6 fold, P < 0.01) and secretion (by sixfold, P < 0.05) of HLA-DR protein, without influencing the accumulation of its mRNA. Alternative splicing, attenuated trafficking, or shedding from the plasma membrane were not observed, but the lysosomal inhibitor bafilomycin A1 reduced HLA-DR secretion. Hypoxia-induced endothelial HLA-DR elevated and diminished the secretion of IL-2 and IL-10, respectively, from co-cultured allogeneic CD4+ T cells in a HLA-DR-dependent manner, as demonstrated by the use of monoclonal anti-HLA-DR. Our results indicate a yet not fully understood post-translational mechanism(s), which elevate both membranal and soluble HLA-DR expression. This elevation is involved in allogeneic T-cell activation, highlighting the pivotal role of ECs in ischemia/hypoxia-associated injury and graft rejection.