An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a gene-centric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently usethe antibodies for systematical analysis of cellular distribution and subcellular localization of proteins in normal and disease tissues. A new version 4.0 of the Human Protein Atlas (www.proteinatlas.org) has been developed in a gene-centric manner with the inclusion of all human genes and splice variants predicted from genome efforts together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide and protein domains and new plots showing the uniqueness (sequence similarity) of every fraction of each protein towards all other human proteins. The new version is based on tissue profiles generated from 6122 antibodies with more than 4 million immunohistochemistry-based images covering 5087 human genes, corresponding to approximately 25% of the human genome. Version 4.0 includes a putative list of members in various protein classes, both functional classes, such as kinases, transcription factors, G-protein coupled receptors etc, and project-related classes, such as candidate genes for cancer or cardiovascular diseases. The exact antigen sequence for the internally generated antibodies is also released together with a visualization of the application-specific validation performed for each antibody, including a protein array assay, Western blot analysis, immunohistochemistry and, for a large fraction, immunofluorescent-based confocal microscopy. New search functionalities have been added to allow complex queries regarding protein expression profiles, protein classes and chromosome location. The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery.