The Cell Atlas provides high-resolution insights into the spatio-temporal distribution of proteins within human cells. The protein localization data is derived from antibody-based profiling by immunofluorescence confocal microscopy, using a panel of 64 cell lines to represent various cell populations in different organs and tissues of the human body. In this cell line panel the mRNA expression of all human genes are characterized using deep RNA-sequencing. The subcellular distribution of each protein is then investigated in a subset of cell lines selected based on corresponding gene expression, and classified into 33 different organelles and fine subcellular structures. The Cell Atlas currently covers 12073 genes (62%) for which there are available antibodies. It offers a database for exploring details of individual genes and proteins of interest, as well as systematically analyzing transcriptomes and proteomes in broader contexts, in order to increase our understanding of human cells.