AIM: To assess the effects of obstructive cholestasis on a wider range of gene expression using microarray technology.METHODS: Male C57BL/6J mice underwent common bile duct ligation (BDL) and were matched with pairfed sham-operated controls. After 7 d, the animals were sacrificed and total RNA was isolated from livers and kidneys. Equal amounts of RNA from each tissue were pooled for each group and hybridized to Affymetrix GeneChip~MG-U74Av2 containing a total of 12488 probe sets. Data analysis was performed using GeneSpringR6.0 software. North analysis and immunofluorescence were used for validation.RESULTS: In sham-operated and BDL mice, 44 and 50% of 12488 genes were expressed in livers, whereas 49 and 51% were expressed in kidneys, respectively.Seven days after BDL, 265 liver and 112 kidney genes with GeneOntology annotation were up-regulated and 113 liver and 36 kidney genes were down-regulated in comparison with sham-operated controls. Many genes were commonly regulated in both tissues and metabolism-related genes represented the largest functional group.CONCLUSION: Following BDL, microarray analysis reveals a broad range of gene alterations in both liver and kidney.