Conjugated linoleic acids (CLAs) have anti-atherogenic effects in both in vitro and animal models. Most studies on CLAs were performed with either a CLA mixture or purified 9cis (Z),11trans (E)-CLA or 10E,12Z-CLA isomers. However, the 9E,11E isomer has superior anti-carcinogenic and anti-inflammatory effects compared with the more abundant CLAs. The 9E,11E-CLA isomer specifically increases interleukin-1 receptor antagonist (IL-1Ra), an important anti-inflammatory mediator that is associated with decreased risk of coronary heart disease. The purpose of this present study was to determine if 9E,11E-CLA affects markers of atherogenesis via regulation of IL-1Ra. In human umbilical vein endothelial cells (HUVECs), 9E,11E-CLA decreased such atherogenesis-related genes as intercellular adhesion molecule-1, vascular cell adhesion molecule-1, monocyte chemoattractant protein-1, E-selectin, P-selectin and C-C motif chemokine receptor-2. Treatment of RAW 264.7 cells with 9E,11E-CLA decreased their adhesion to HUVECs. This effect was reversed by inhibiting the phosphoinositide 3-kinase or mouse target of rapamycin pathways. IL-1Ra-deficient RAW 264.7 cells (siIL-1Ra RAW) bind more efficiently to HUVECs compared with the control stable cells (si-control RAW). In addition, HUVECs treated with siIL-1Ra RAW-conditioned media induce significantly higher levels of intercellular adhesion molecule-1, vascular cell adhesion molecule-1, monocyte chemoattractant protein-1 and E-selectin than HUVECs treated with si-control RAW-conditioned media. Taken together, the data show that 9E,11E-CLA decreases the atherogenesis-related genes in HUVECs and alters adhesion of macrophages. In addition, the induction of IL-1Ra by 9E,11E-CLA is partially responsible for the anti-atherogenic properties of this particular CLA isomer.