In the present study we analyzed changes in the pattern of gene expression in endothelial cells (HUVEC) exposed to elevated homocysteine levels under flow conditions. RNA samples of untreated and homocysteine treated EC were analyzed using a human cDNA array containing 588 cDNAs relevant to the cardiovascular system. Exposure to homocysteine under flow resulted in altered expression of 8 genes, the alterations of 3 of which were further confirmed by RT-PCR analysis: upregulation of MCP-1 and of profilin-I, and downregulation of alpha-catenin. The increased expression of profilin-I and the decreased expression of alpha-catenin were also confirmed at the protein level by Western blot analysis. Furthermore, immunostaining for alpha-catenin demonstrated complete loss of the protein from intercellular junctions following exposure to homocysteine under flow. All these changes were not observed in cells exposed to homocysteine under static conditions. We show that under flow conditions, homocysteine modulates the expression of genes/proteins involved in actin cytoskeleton reorganization, as well as in the formation and/or maintenance of cell-cell junction, thus contributing to the morphological changes (e.g. cell retraction) reflecting endothelial cell injury.