The expression of thousands of genes can be monitored simultaneously using cDNA microarray technology. This technology is being used to understand the complexity of human disease. One significant technical concern regards potential alterations in gene expression because of the effect of tissue ischemia. This study evaluates the increase in the differential gene expression because of tissue processing time. To evaluate differential gene expression because of ischemia time, prostate samples were divided into five time points (0, 0.5, 1, 3, and 5 hours). Each time point consisted of a homogeneous mixture of 12 to 15 prostate tissue cubes (5 mm(3)). These tissues were maintained at room temperature until at the assigned time point the tissue was placed in OCT, flash frozen in liquid nitrogen, and stored at -80 degrees C until RNA extraction. RNA from each time point was hybridized against an aliquot of 0 time point RNA from the same prostate. Four prostate glands were used in parallel studies. M-A plots were graphed to compare variability between time point sample hybridizations. Statistical Analysis of Microarray software was used to identify genes overexpressed at the 1-hour time point versus the 0-hour time with statistically significance. Microarray analysis revealed only a small percentage of genes (<0.6%) from more than 9000 to demonstrate overexpression at the 1-hour time point. Among the 41 statistically significant named overexpressed genes at the 1-hour time point were early growth response 1 (EGR1), jun B proto-oncogene (jun B), jun D proto-oncogene (jun D), and activating transcription factor 3 (ATF3). Genes previously associated with prostate cancer did not have significantly altered expression with ischemia time. Increased EGR1 protein expression was confirmed by Western blot analysis. Microarray technology has opened the possibility of evaluating the expression of a multitude of genes simultaneously, however, the interpretation of this complex data needs to be assessed circumspectly using refined statistical methods. Because RNA expression represents the tissue response to insults such as ischemia, and is also sensitive to degradation, investigators need be mindful of confounding artifacts secondary to tissue processing. All attempts should be made to process tissue rapidly to ensure that the microarray gene profile accurately represents the state of the cells and confirmatory studies should be performed using alternative methods (eg, Northern blot analysis, Western blot, immunohistochemistry).