In the evolving era of “big data”, integration of datasets from different omics technologies have received increased attention, paving the way for further progress in molecular medicine and targeted treatment. The Human Protein Atlas database (www.proteinatlas.org) based on integration of transcriptomics, antibody-based imaging, mass spectrometry and systems biology constitutes the largest knowledge resource for spatial localization of proteins in organs, tissues, cells and organelles. Divided into six different parts, it covers a wide spectrum of protein localization at different levels. The Tissue Atlas1 shows the distribution of proteins across all major human tissues and organs, and recent updates include a new classification of all human genes based on tissue specificity and distribution, using a combination of three different transcriptomics datasets. Other additions involve characterization of proteins selectively expressed in rare tissues2, and single cell evaluation of >500 proteins elevated in testis3. The Cell Atlas4 focuses on subcellular localization of proteins in single cells, and the Pathology Atlas5 presents the consequence of all human genes on patient survival in cancer. Three new parts were added in September 2019; the Blood Atlas displaying transcriptomic profiles of human blood cells and concentration levels of proteins in blood; the Brain Atlas showing the distribution of proteins in human, mouse and pig brain; and the Metabolic Atlas summarizing the presence of metabolic pathways across human tissues. The Human Protein Atlas database has several potential implications for use in medicine, and constitutes an important starting point for identification of candidate proteins that may contribute to further understanding of disease mechanisms, aid in stratifying high-risk individuals, and guide treatment modalities. In summary, the Human Protein Atlas is a comprehensive stand-alone open-access resource available for researchers worldwide, and is believed to help accelerating efforts meeting future needs in personalized healthcare, and leading to products that will benefit humanity.