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1.Background: Personalized Medicine requires tools that allow to investigate the expression of molecular markers, in particular of signal transduction cascades, on the single-cell level to understand the mechanisms of tumor formation.Proper definition and understanding of cellular interactions and molecular interdependencies is crucial for patient-specific, i.e.mechanism-specific therapy selection.High-throughput tissue cytometry by TissueFAXS provides the level of cellular details that is required for investigating specialized therapy options and case-specific therapy requirements.2.Technology and Method: The TissueFAXS system is an automated tissue cytometer providing fast slide-scanning as well as sophisticated image analysis.The samples can be stained by means of immunohistochemistry or immunofluorescence.By using a nuclear marker the location of the individual cells is identified and the system quantifies the staining intensity in each color channel for each and every cell.It allows even to distinguish and compare between nuclear, cytoplasmatic, as well as membrane marker expression in the same sample.Also meta-structures consisting of higher levels of cellular organisation (e.g.tumor formations, glands, etc.) can be recognized automatically and compared to the cellular level.3.Results: Results presented come from several studies and comprise different applications of highthroughput tissue cytometry.(i) Early diagnosis of prostate cancer using markers CD45, CD 15,CD31, p63, and AMACR; (ii) quantification of proliferation marker Ki67 and Her2 in breast cancer;and (iii) breakthrough finding [2012 Nov; 18(11): 1699-704] by high-throughput tissue cytometry leading to a novel therapeutic intervention in aggressive non-Hodgkins lymphoma.4.Discussion: The studies shown demonstrate novel approaches in personalized medicine enabled by high-throughput tissue cytometry.Observer independence and reproducible measurements on the single-cell level are especially important in definition and selection of patient-specific clinical interventions.