A specialized brain vasculature is key for establishing and maintaining brain interstitial fluid homeostasis, which for most amino acids (AAs) are ∼10% plasma levels. Indeed, regulation of AA homeostasis seems critical for normal central nervous system functions, and disturbances in brain levels have both direct and indirect roles in several neuropathologies. One mechanism contributing to the plasma to brain AA gradients involves polarized expression of solute carrier (SLC) family transporters on blood-brain barrier (BBB) endothelial cells. Of particular interest is the localization of sodium-dependent transporters that can actively move substrates against their concentration gradient. In this study, the in vivo endothelial membrane localization of the sodium-dependent glutamine transporters Snat3 (Slc38a3) and Snat1 (Slc38a1) was investigated in the mouse brain microvasculature using immunofluorescent colocalization with cellular markers. In addition, luminal membrane expression was probed by in vivo biotinylation. A portion of both Snat3 and Snat1 vascular expressions was localized on luminal membranes. Importantly, Snat1 expression was restricted to larger cortical microvessels, whereas Snat3 was additionally expressed on BBB capillary membranes. This differential expression of system A (Snat1) versus system N (Snat3) transporters suggests distinct roles for Snats in the cerebral vasculature and is consistent with Snat3 involvement in net transendothelial BBB AA transport.