DNA microarray represents one of the major advances in functional genomics. Its ability to study expression of several thousands of genes or even all genes in the entire genome in a single experiment has changed the way in which we address basic biomedical questions. Numerous publications have shown its utility in drug discovery, disease diagnosis, novel gene identification, and understanding complex biological systems. However, there are substantive technical issues associated with the use of this technology that limit the interpretation of microarray data. In this review, we first give an overview of DNA microarray technology and then focus on uncertainty areas of microarray technology that include making microarrays, isolation of RNA and labeling, hybridization and scanning, and data analysis. The center theme of this review is to improve microarray reproducibility by addressing common technical problems. Finally, we briefly summarize microarray's applications in biomedical research.