To examine the early changes in gene expression levels in lung tissues by cDNA microarray using a rat model of total hepatic ischemia reperfusion and to analysis function of the changes.Twelve adult male SD rats weighting 220 - 250 g were divided randomly into two groups (6 in each group). The rats were sacrificed at end point of the operation and lung tissues were divided into several parts for either microarray analysis or RT-PCR of several genes selected from microarray data. Common change genes were selected from three chips and the final results of microarray analysis were identified by RT-PCR. At last, differentially expressed genes were classified according to their biological functions by cluster analysis.Analysis of the results showed those 48 genes up-regulated and 32 genes down-regulated after hepatic ischemia reperfusion lung injury. Only parts of them had we known about the function. Genes significantly up-regulated were IL-1 alpha, IL-1 beta, SLPI, MMP9, MMP14, MMP15, TIMP1, PIK3RL, MAPK, NF-kappaB, JNK and others. Genes significantly down-regulated were CYP1A1, NQO1, GSTA3, RETNLA and others. Differentially expressed genes were mainly classified into inflammatory reaction, transcription factors, cell metabolism, signals transduction, ion or receptors, cytoskeleton, etc.cDNA microarray technique provides a new method for detecting differentially expressed genes in rat lung tissues. Further study may reveal the molecular pathologic mechanism of hepatic ischemia reperfusion lung injury and discern new targets for therapeutic interventions.