Dietary isoflavones are considered to be cardioprotective because of their structural similarity to estrogen. Equol is a metabolite of daidzein that is more potent than daidzein itself. The effect of equol on endothelial function and oxidative stress remains unclear. The objective of this study was to determine the effect of 100 mg/day soy isoflavone supplementation on the following markers: vascular cell adhesion molecule-1 (VCAM-1) and nitric oxide (NO) as markers of vascular endothelial function, and malonyldialdehyde (MDA) as oxidative stress marker in equol-producing postmenopausal women. A stratified randomized double blind controlled trial was conducted among 190 postmenopausal Indonesian women aged 47 to 60 years. They were stratified into equol producers and equol nonproducers. The random allocation of intervention was carried out separately in each stratum. The intervention group received tablets consisting of 100 mg soy isoflavones and calcium carbonate 500 mg, and the control group received 500 mg calcium carbonate. The concentrations of VCAM-1, NO and MDA were measured at baseline and post-supplementation at 6 months. After 6 months of supplementation the MDA concentrations were significantly lower in the soy-isoflavone equol producers compared with equol nonproducers (p=0.021). Similar results were also found for VCAM-1 and NO concentrations, but these were statistically not significant (p = 0.413 and p= 0.724, respectively). This study demonstrates that isoflavone supplementation in postmenopausal women with equol-producer status had a more beneficial effect by decreasing the MDA concentration, but did not improve VCAM-1 and NO concentrations.