The detection, diagnosis, and management of breast cancer rely on an integrated approach using clinical history, physical examination, imaging, and histopathology. The discovery and validation of novel biomarkers will aid the physician in more effectively achieving this integration. This review discusses efforts in surface-enhanced laser desorption/ionization (SELDI)-based proteomics to address various clinical questions surrounding breast cancer, including diagnosis, monitoring, and stratification for treatment. Emphasis is placed on examining how study design and execution influence the discovery and validation process, which is critical to the proper development of potential clinical tests.