DNA rnicroarrays are powerful tools for the high throughput analysis of nucleic acids due to their parallel detection capabilities. To realize the apparent power of DNA microarray, an efficient assay format is essential and a variety of assay formats have been developed for nucleic acid detection on microarrays. Many of them employ fluorescence-based methods because fluorescence detection is straightforward and easy to implement. Herein we broadly review fluorescence-based assay formats with a focus on PCR-associated target preparation. For the heterogeneous assay of nucleic acid on DNA microarrays, sensitivity is one of the most important factors and special emphasis has been given to recently developed signal amplification strategies aimed at achieving high sensitivity. (c) 2005 Elsevier Ltd. All rights reserved.