Analysis of the transcriptome using DNA microarrays has become a standard approach for investigation of the molecular basis of human disease in both clinical and experimental settings. However, drawing conclusions from the wealth of data obtained has remained problematic. There have been difficulties with accurate reporting of results, with experimental reproducibility and with identifying and interpreting the biologically relevant information. In this review we discuss the successful use of DNA microarray technology in molecular medical research, and we highlight methods of addressing the issues of both reproducibility and biological interpretation.