Purpose To establish the patter of expression for 11 solute carrier (SLC) and 28 phase II conjugation enzymes belonging to the 7 families of conjugation enzymes from human isolated brain microvessels and from the hCMEC/D3 immortalized human cerebral microvascular endothelial cell line Methods We used SYBR Green fluorescence detection real time quantitative RT-PCR, ABI Prism 7900 HT Sequence Detection System® to establish the pattern of mRNA expression. Specimens of brain cortex from 7 patients underwent surgery for epilepsia and glioma were considered healthy based on neuroimaging. Microvessels were isolated, mRNA was extracted and cDNA library was prepared from each patient to be compared with the corresponding cerebral cortex using the delta-deltaCt method. Similarly, mRNA was extracted and cDNA libraries were prepared from hCMEC/D3 immortalized human cerebral microvascular endothelial cell line to be compared with Human Umbilical Vein Endothelial Cells (HUVEC). Results SLC7A5 and SLC2B1 were the main transporters expressed (61.2% and 29.2%) and were 13 and 9.5 folds more expressed than in cortex. In hCMEC/D3, SLC16A1 and SLC7A5 were the main genes expressed (55.3% and 41.9%). HUVEC expressed similar pattern with the exception of SLCO2B1, which was not detectable in hCMEC/D3. Microvessels and cerebral cortex expressed different patterns of phase II enzymes. However, glutathione S-transferase (GSTM1), sulfotransferase (SULT4A1), methyltransferases (PRMT8), and N-acetyltransferase (NAT1) were detected in cortex only. Comparable expression was established in hCMEC/D3 and HUVEC. Conclusion Expression profiles of SLC transporters and phase II conjugation enzymes comparing the pattern of expression at the BBB and cerebral cortex, hCMEC/D3 and HUVEC were established. Microvessels expressed more SLC transporters than cerebral cortex. Among the sulfotransferases tested, only SULT1A1 was detected in microvessels and cerebral cortex, similarly in hCMEC/D3 and HUVEC samples. None of the UDP-glucuronosyltransferases (UGTs) or dopa decarboxylases (DDC) tested were detectable. However, they were detected only in human liver samples used as positive control.