Various gene expression DNA microarray platforms have been developed and often similar experiments are conducted using different types of arrays. Several investigators have explored the cross-platform comparison issues and reached mixed conclusions, ranging from discrepant to reasonably concordant results across platforms. These comparative studies, however, did not apply rigorous sequence-matching criteria. Since the sample size in each experiment is small, combining the information may help increase statistical power. Here we address this issue using the probe sequences to determine matching probes. Smooth muscle cells from the thoracic aorta of C57B46J mice treated with benzo(a)pyrene or dimethyl sulfoxide were examined using GeneChip and CodeLink arrays. Corresponding probes on the two platforms were identified by stand-alone BLAST. In general, CodeLink selected more genes as differentially expressed. For GeneChip arrays, among the various algorithms considered, more probe sets were found significantly changed using the MAS 5.0 expression estimates. The Li-Wong PM-only expression estimates led to fewer discordant results between the two platforms. We conducted quantitative RT-PCR assays on several genes to further assess the performance of each platform. We found that the use of different expression estimation algorithms led to different results within the same platform. The qRT-PCR experiments did not consistently confirm the results of either platform.