The Human Protein Atlas (HPA) was initiated in 2003 and aims to map all protein-coding genes in human tissues and cells. Transcriptomics data and antibody based protein localization is integrated and publicly available in an open access knowledge resource (www.proteinatlas.org). In 2015 we published an expression based tissue classification, identifying 1684 genes as brain elevated compared to all other tissue types. Since then, external data has been integrated and additional RNAseq analysis added, including the pig and mouse brains. These efforts aim to achieve a complete overview capturing the complex molecular organization of the brain. All integrated data of various sources, are now combined into a brain-centric sub atlas as part of the HPA. Quantitative RNA expression profiles provide regional overview of human, pig and mouse brain, enabling species comparison across the different brain regions. Global expression comparisons show a clustering of the brain regions related to the developmental origin, the regions of brainstem and cerebrum are for instance separated. By investigating regional specific expression we learned that cerebellum is the most unique brain region from multiple perspectives, both between regions as well as between species. In addition, we also identified several species differences related to the olfactory system. Although most neurotransmitter systems are well preserved between the species we identified several receptor genes with a different regional expression profile when comparing species, highlighting the importance of species comparison and verification when selecting a relevant animal model. All expression data as well as protein profiles for selected targets can be found on gene specific pages at www.proteinatlas.org/brain (which is released the first week of September 2019). Additionally, interactive summary pages provide an exploratory platform to further investigate regionally elevated expression, cell type related proteins and brain elevated expression in the human body.