The activation of peroxisome proliferator activated receptor-gamma (PPARgamma) ameliorates the homocysteine (Hcy)-induced matrix metalloproteinase (MMP) by decreasing reactive oxygen species (ROS) production. However, the mechanism by which Hcy induces ROS generation and MMP activation is unclear. We hypothesize that Hcy increases NADH oxidase (Nox-4) and decreases thioredoxin (Trx). This leads to translocation of Nox-4 into the mitochondria and decrease in Trx. In addition, activation of PPARgamma ameliorates the translocation of Nox-4 into mitochondria and MMP-9 activation. Mouse aortic vascular endothelial cells (MVEC) were cultured in the presence or absence of 100 microM Hcy. The cells were pre-treated with ciglitazone (CZ, 150 microM). Activity of PPARgamma activity was measured by electrophoretic mobility shift assay (EMSA) and antibody super shift assay. In situ generation of ROS was measured using 2,7-dichlorofluorescin (DCF) as a probe. The expression of Nox-4 and Trx were measured by quantitative real-time polymerase chain reaction (Q-RT-PCR). The translocation of Nox-4 was measured by 2-D gel analysis. To determine the levels of Nox-4 and Trx, the mitochondria and cytosol were separated and Western blot analysis was preformed. The MMP-9 activity was measured by gelatin-zymography. The results suggested that CZ activated endothelial PPARgamma in the presence of Hcy. Production of ROS was ameliorated by PPARgamma activation. Expression of Nox-4 was increased, while production of Trx was decreased by Hcy. However, the treatment with CZ normalized the levels of Nox-4 and Trx. Nox-4 was translocated into mitochondria in Hcy-treated endothelial cells. This translocation was associated with decreased production of Trx in mitochondria. The treatment with CZ blocked this translocation and increased Trx levels in mitochondria. Hcy-mediated MMP-9 activity was decreased in cells pre-treated with CZ. These results suggest that Hcy increases NADH oxidase and decreases Trx by translocation of Nox-4 to mitochondria. The data show that indeed, activation of PPARgamma ameliorates the mitochondrial translocation of NOX-4 and MMP-9 activation.