Blood-brain barrier (BBB) genomics begins with the isolation of capillaries from fresh animal or human brain and is followed on the same day with the purification of capillary-derived RNA. The identification of microvascular-enriched genes from a whole brain gene microarray is unlikely because the brain capillary endothelial volume is <0.1% of total brain. Libraries of partial cDNAs corresponding to genes that are selectively expressed at the BBB are generated with polymerase chain reaction–based approaches such as subtractive suppressive hybridization. The availability of these partial cDNAs, in conjunction with production of animal or human BBB cDNA libraries, enables the cloning of the full-length cDNAs and a functional analysis of the BBB-enriched genes. The development of BBB genomics technologies enables the acquisition of a large body of new knowledge about the BBB and the brain microvasculature.