Arterial endothelial phenotype heterogeneity significantly influences athero-suceptibility and athero-protection in vivo. Differential transcript profiling of endothelium in susceptible arterial regions of normal adult swine displays a balance of pro-pathological and protective transcript profiles when compared with adjacent regions that rarely, if ever, develop atherosclerosis. The endothelial phenotype in vivo and in vitro is highly sensitive to the local blood flow characteristics via mechanotransduction and transport mechanisms. Athero-susceptible locations map to regions of hemodynamic (and biomechanical) spatio-temporal complexity where transient vortices within flow separation zones promote flow reversal, oscillatory shear stresses, low flow velocities and low mean shear stresses, steep spatial shear stress gradients, and occasional turbulence (chaotic flow). Differential phenotypes are detectable in endothelium in vivo at the mRNA, protein, post-translational, and functional levels. We now demonstrate that differential microRNA expression that targets specific gene and protein expression is part of the regulation of endothelial phenotype. Regulation of mRNA stability and translation occurs by highly conserved small non-coding microRNAs (miRNAs). Microarrays identified 3 miRNA families (let-7, miR10, miR26) as upregulated in endothelium from an atheroprotected region of thoracic aorta relative to a nearby atherosusceptible region (aortic arch). By qRT-PCR, expression levels of miR10a and 10b were 4.9 and 20.7-fold higher respectively at protected (n=8) vs susceptible (n=10) regions; in contrast miR7d and miR26b were elevated <2-fold. The copy number of miR10a was greater than that of miR10b and its preferential expression in endothelium in situ was detected by immunofluorescence. 854 putative targets of miR10a/b were organized into interactive pathways using IngenuityTM. Sequences of 138 of the most interactive genes were entered into the Sfold program that assesses target secondary structure as an important predictor of miRNA-target hybridization sensitivity. Among miR10a/b targets showing high total hybridization energy were Flt-1 (VEGFR1), Hox-D10 and VEGFA. Endothelial expressions of these genes were suppressed in protected vs susceptible regions in a reciprocal relationship with miR10a/b. Cultured endothelial cells overexpressing miR10 suppressed Flt-1 gene expression. The data show miRs to be flow responsive and suggest miR10a/b to be important regulators of endothelial gene expression in atheroprotection/susceptibility.