Pharmacogenomics is defined as identification of loci which are involved in determining the responsiveness and distinguishing responders and non-responders to a given drug. Genome sequencing, transcriptome and proteome analysis are of particular significance in pharmacogenomics. Sequencing is used to locate polymorphisms, and monitoring of gene expression can provide clues about the genomic response to disease and treatment. The transcriptome analysis can be done by methods of random cDNA sequencing (expressed sequence tag project, body map project, serial analysis of gene expression, etc.), mRNA display (differential display, fluorescent differential display, RNA arbitrary primed PCR, molecular indexing, gene expression fingerprinting, etc.) and differential hybridization (cDNA high density filter, cDNA microarray, oligomicrochip, etc.). We describe the principle and application of trancriptome analysis in pharmacogenomics, especially differential display and cDNA microarray. We used transcriptome analysis to identify therapeutic target genes by studying the change of gene expression in animal models of oxidative stress and hypoxia and found novel drug target candidates through this pharmacogenomic strategy.