Peroxisome proliferator-activated receptor type gamma (PPAR) is a subgroup of the PPAR transcription factor family. Recent studies indicate that loss of PPAR is associated with the development of pulmonary hypertension (PH). We hypothesized that the endothelial dysfunction associated with PPAR inhibition may play an important role in the disease process by altering cellular gene expression and signaling cascades. We utilized microarray analysis to determine if PPAR inhibition induced changes in gene expression in pulmonary arterial endothelial cells (PAEC). We identified 100 genes and ESTs that were up-regulated by > 1.5-fold and 21 genes and ESTs that were down-regulated by > 1.3-fold (P< 0.05) by PPAR inhibition. The up-regulated genes can be broadly classified into 4 functional groups: cell cycle, angiogenesis, ubiquitin system, and zinc finger proteins. The genes with the highest fold-change in expression: hyaluronan-mediated motility receptor (HMMR), VEGF receptor 2 (Flk-1), Endothelial PAS domain protein 1 (EPAS1), basic fibroblast growth factor (FGF-2), and caveolin-1 in PAEC were validated by real time RT-PCR. We further validated the up-regulation of HMMR, Flk-1, FGF2, and caveolin-1 by Western blot analysis. In keeping with the microarray results, PPAR inhibition led to re-entry of cell cycle at G1/S phase and cyclin C up-regulation. PPAR inhibition also exacerbated VEGF induced endothelial barrier disruption. Finally we confirmed the down-regulation of PPAR and the up-regulation of HMMR, Flk-1, FGF2, and Cav-1 proteins in the peripheral lung tissues of an ovine model of pulmonary hypertension. In conclusion, we have identified an array of endothelial genes modulated by attenuated PPAR signaling which may play important roles in the development of pulmonary hypertension.