Although infection of Porphyromonas gingivalis (P. gingivalis) is closely correlated with progress of vascular inflammatory diseases, distinctive pathogenesis induced by P. gingivalis is still elusive. We investigated the impact of P. gingivalis lipopolysaccharide (P. gingivalis-LPS) on gene expression in endothelial cells with comparison to Escherichia coli lipopolysaccharide (E. coli-LPS) and zymosan. Here, we showed that the expressions of interleukin-6 and tumor necrosis factor-α mRNA induced by P. gingivalis-LPS are much lower than those by E. coli-LPS, and that the expressions of interleukin-8 and hypoxia inducible factor-2α are also lower than those by zymosan. These effects of P. gingivalis-LPS-mediated alterations of gene expression were cancelled in the absence of fetal bovine serum in culture medium. Of note, P. gingivalis-LPS treatment reduced the gene expressions of tissue factor and plasminogen activating inhibitor-1 as opposed to either E. coli-LPS or zymosan treatment. Our finding suggests that alterations of gene expression pattern in endothelial cells mediated by P. gingivalis-LPS may contribute to the pathogenesis of vascular inflammatory diseases.