Development of new array-based technologies enabled complex analysis of genome, transcriptome and proteome in health and disease. Its results appear to induce dramatic changes in cancer research and show the advent of molecular medicine. Genomic studies are logically extended by including proteomic studies allowing early detection of pathological malignant processes in tissues and corresponding changes in serum protein spectrum. The ProteinChip® technology based on SELDI-TOF mass spectrometry is a new proteomic technology providing a quantitative proteomic approach in biomarker studies. Its principles, application potential and limitations in functional and diagnostic proteomics and molecular medicine are discussed.