The combined action of multiple cell types is essential for the physiological function of the lung, and increased awareness of the molecular constituents characterizing each cell type is likely to advance the understanding of lung biology and disease. In the current study, we used genome‐wide RNA sequencing of normal lung parenchyma and 26 additional tissue types, combined with antibody‐based protein profiling, to localize the expression to specific cell types. Altogether, 221 genes were found to be elevated in the lung compared with their expression in other analyzed tissues. Among the gene products were several well‐known markers, but also several proteins previously not described in the context of the lung. To link the lungspecific molecular repertoire to human disease, survival associations of pneumocyte‐specific genes were assessed by using transcriptomics data from 7 nonsmall‐cell lung cancer (NSCLC) cohorts. Transcript levels of 10 genes (SFTPB, SFTPC, SFTPD, SLC34A2, LAMP3, CACNA2D2, AGER, EMP2, NKX2‐1, and NAPSA) were significantly associated with survival in the adenocarcinoma subgroup, thus qualifying as promising biomarker candidates. In summary, based on an integrated omics approach, we identified genes with elevated expression in lung and localized corresponding protein expression to different cell types. As biomarker candidates, these proteins may represent intriguing starting points for further exploration in health and disease.—Lindskog, C., Fagerberg, L., Hallström, B., Edlund, K., Hellwig, B., Rahnenführer, J., Kampf, C., Uhlén, M., Pontén, F., Micke, P., The lung‐specific proteome defined by integration of transcriptomics and antibody‐based profiling. FASEB J. 28, 5184–5196 (2014). www.fasebj.org