Objective To investigate the changes of gene expression in the cardiac outflow tract (OFT) in Cx43 knockout mouse embryo, and to elucidate the genes involved in the pathogenesis of pulmonary outflow obstruction. Methods The cDNA was retrotranscripted from RNA extracted from OFT tissues of both Cx43 knockout and Cx43 wild type mouse embryos on embryonic day (ED) 14.5. The biotin-labeled cRNA derived from the transcription of cDNA was fragmented as probes. The probes were hybridized with Affymetrix Mouse Genome 430 2.0 Array. Gene Array Scanner was used to screen the signals of hybridization and the expression of genes was detected. Results Among the differentially expressed genes, there were 287 upregulated and 199 downregulated in Cx43 knockout OFT tissue as compared with those in Cx43 wild type heart. Functions of proteins encoded by the altered genes encompassed all functional categories, with largest percentage in genes involved in regulation of transcription, cell cycle, etc. Among the differentially expressed genes in the Cx43 knockout heart were those related to Galpha13 signaling pathway. Conclusions Genes related with Galpha13 signaling pathway differently expressed in ED14.5 Cx43 knockout OFT tissue may be involved in the pathogenesis of pulmonary outflow obstruction.