The transcriptional response of skeletal muscle to chronic corticosteroid exposure was examined over 168 hours and compared to the response profiles observed following a single dose of corticosteroid. Male adrenalectomized Wistar rats were given constant rate infusion of 0.3 mg/kg/h methylprednisolone for up to 7 days via subcutaneously implanted mini-pumps. Four control and 40 drug-treated animals were sacrificed at 10 different time points during infusion. Liver total RNAs were hybridized to 44 individual Affymetrix REA230A gene chips. Previously we described a filtration approach for identifying genes of interest in microarray datasets developed from tissues of rats treated with methylprednisolone following acute dosing. Here, a similar approach involving a series of 3 filters was applied sequentially in order to identify genes of interest. These filters were designed to eliminate probe sets that were not expressed in the tissue, not regulated by the drug, or did not meet defined quality control standards. Filtering eliminated 86% of probe sets, leaving a remainder of 2316 for further consideration. In a previous study, 653 probe sets were identified as MPL-regulated following administration of a single (acute) dose of the drug. Comparison of the two datasets yielded 196 genes identified as regulated by MPL in both dosing regimens. Due to receptor down-regulation, it was predicted that genes regulated by receptor-GRE interactions would exhibit tolerance in chronic profiles. However, many genes did not exhibit steroid tolerance, indicating that current perspectives on the mechanism of glucocorticoid action cannot entirely explain all temporal profiles.