Blood-brain barrier (BBB) membrane proteins play crucial roles in the proper functioning of the BBB as well as in disease progression. Previously, we developed a novel approach for identifying membrane proteins expressed at the BBB, which we referred to as multiplex expression cloning. In this study, the proteome coverage of the multiplex expression cloning approach was expanded to allow the identification of a total of 30 BBB membrane proteins that are diverse in function and abundance. To unveil those membrane proteins that are enriched at the BBB and hence partially responsible for some of its unique characteristics, the transcript abundance levels for all 30 BBB membrane proteins were compared with those found in microvessels derived from lung, liver, heart, and kidney. Such quantitative PCR profiling of RNA samples from laser capture microdissected microvessels revealed that the transcripts for five membrane proteins, namely Lutheran glycoprotein, carbonic anhydrase IV, uncoupling protein 2, podocalyxin, and solute carrier family 38, member 5, were BBB selective, in that expression was elevated in brain microvessels when compared with all of the vascular beds tested. Many other membrane protein transcripts, whereas not as BBB-restricted, showed selective expression within subsets of tissues indicating other potential parallels and contrasts between vascular beds in the body. The identification of BBB membrane proteins could help better understand the molecular mechanisms responsible for BBB function and those with selective expression may have utility for BBB-targeted therapies.