Purpose: To establish a comprehensive proteomic approach for biomarker discovery and validation in breast fluid. Experimental Design: A total of 95 specimens from three institutions were used including 10 nipple aspiration fluid (5 stage I/II cancerous breasts and 5 age-matched healthy controls), 42 ductal lavage fluid from 14 patients with unilateral stage I/II cancer (25 from 9 cancerous breasts and 17 from 7 contralateral breasts), and 42 ductal lavage fluid from 14 high-risk women (multiple ducts repeated lavage). Differentially expressed protein/peptides were discovered by proteomic analysis of training sample, using ProteinChip arrays and surface-enhanced laser desorption ionization (SELDI) time-of-flight mass spectrometry, and validated on independently collected testing samples. After protein identification, ELISA was done to confirm the SELDI findings. Results: We were able to obtain reproducible protein profiles using minimal amount of protein (1 Ag) by applying an optimized chip protocol and SELDI.We were able to select cancer-associated biomarkers despite large individual variability by applying both unsupervised and supervised cluster analysis. Furthermore, we were able to train and test candidate biomarkers on independently collected samples and identified one component of a multimarker panel as human neutrophil peptides 1to 3. Conclusions: Breast fluid is a rich source of breast cancer biomarkers. In combination with highthroughput novel proteomic profiling technology and multicenter study design, markers that are highly specific to breast cancer can be discovered and validated. Our observations also suggest that persistent elevation of human neutrophil peptide in high-risk women may imply early onset of cancer not yet detectable by current detection method. Proof of this hypothesis requires follow-up on a larger study population.Breast cancer is the most commonly diagnosed cancer among women. Presymptomatic screening to detect early-stage breast cancer while it is still resectable could potentially reduce breast cancer-related mortality. Unfortunately, only 63% (1992-1999, United States) of the breast cancers are localized at the time of diagnosis (1). Small lesions are frequently missed and may not be visible even by mammography, particularly in young women and women with dense breast tissue (2). Molecular markers that can potentially identify these small lesions that are invisible to imaging techniques will provide a real opportunity to treat a neoplasm before it invades the tissue.Breast cancer is highly heterogeneous. Most molecularly based approaches that have been investigated for the early detection of breast cancer are targeted at specific factors, such as oncogenes, tumor suppressor genes, growth factors, tumor antigens, or other gene products. The inherent problem is that none of these factors alone can account for a large majority of the breast cancers and some are not specific to cancer or breast tissues; thus, the sensitivity and specificity of such approaches is low. Thus f...