Objective:To screen differentially expressed genes in rat glomerular mesangial cells(GMCs)in response to sublytic C5b-9 by microarray of high flux. Methods:Rat primary GMCs were cultured and stimulated with or without sublytic C5b-9, then the total RNA in GMCs was extracted,and the RNA was reversely transcribed to biotinylated labeled cDNA probes. The mixed probes were hybridized for cDNA microarray. Then, the chips were subsequently scanned by Affymetrix Scanner 3000 and read with software GCOS1.4. Then differentially expressed genes were identified and annotated to Gene Ontology(GO)database in order to analyze these genes function. Results:The results showed that among expression profile of 31 000 genes, up-regulated and down-regulated genes over 2 folds under sublytic C5b-9 attacking for 40 min were 4 124 and 2 234, and were 4 512 and 2 859 under attacking for 3 h respectively. Meanwhile, there were 2 325 genes up-regulated and 1 419 genes down-regulated over 2 folds under sublytic C5b-9 attacking for 40 min or 3 h. Analysis of these differences of genes function by GO, these differentially expressed genes function mainly involved in regulation of biological process, biological regulation, localization,response to stimulus, developmental process,proliferation, metabolic process,cellular process, multicellular organismal process and so on. Conclusion:sublytic C5b-9 stimulating rat GMCs indeed could cause the changes of gene expression.