Chronic kidney disease (CKD) is a global health problem. There is a need for early detection, diagnostic and progression biomarkers, which could identify the disease in its early stages, when treatments are more effective. Integration of experimental results followed by an extensive data analysis and mining could lead to the discovery of such novel biomarkers. The peptiCKDdb is a repository of manually curated peptidomics and proteomics datasets extracted from scientific publications related to CKD. It can serve as a knowledge base for scientists seeking confirmation of their findings, as well as a source of data for integrative analysis supporting biomarker research in the field of renal pathology.