With recent advances in the knowledge of human molecular genetics, new gene-based disease mechanisms are emerging in many areas of medicine. The study of new prognostic and diagnostic markers in large numbers of clinical specimens is an important step in translating the new findings from basic science to clinical practice. The recently developed tissue microarray technology allows parallel molecular profiling of clinical samples at the DNA, RNA, and protein level. This technique enables pathologists to perform large-scale analyses using immunohistochemistry, fluorescence in situ hybridization, or RNA in situ hybridization substantially faster and at markedly lower costs compared with the conventional approach. This article provides a short review of this technology, focuses on several technical aspects of tissue microarray construction, and addresses the validity of the tissue microarray results for clinical research by reviewing data from recent literature along with the authors' own data.