To accelerate study of gene function, a home-made high-density cDNA microarray was developed, using the cDNA clones from different types of tissues. In order to cover as far as possible the whole genome, cDNA clones that essentially represented genes with low abundance were introduced from Resgene Company. Totally 384 quality control DNA and 12 630 cDNA fragments, which includes 12 508 Unigenes and 122 ESTs, were spotted on the chip, after optimization. The home-made cDNA microarray was evaluated with Microarray ScoreCard and proved to be representative and reliable. These microarrays were then used to study the differential gene expression profiles of visceral adipose tissues between obese patients and normal subjects. The results showed that genes involved in immune-regulation, apoptosis and metabolism of energy were up-regulated in obese patients, while genes involved in lipid synthesis were down-regulated in obese patients. Further exploration of these genes will greatly improve the understanding of the pathogenesis of obesity.