Gap junctions are vital for cellular integrity, including homeostasis, morphogenesis, differentiation and growth in normal development of organs such as heart. Connexin 43 (Cx43) is a major gap junction protein. Our cDNA microarray analysis of normal and nitrofen-exposed neonatal mice with hypoplastic lungs, associated congenital diaphragmatic hernia (CDH) and heart developmental defects showed up-regulation of Cx43. Our objective was to establish if cardiopulmonary defects in nitrofen-exposed mice may be linked to altered expression of the Cx43 gene. We addressed our objective by performing northern blot analysis, real-time RT-PCR, immunoblotting and immunohistochemistry by localizing Cx43 in hearts and lungs of normal and nitrofen-exposed mice at different gestational stages. The data confirmed up-regulation of Cx43 expression in both hearts and lungs of CDH neonate mice and in lungs at other developmental stages except the pseudoglandular stage. However, Cx43 protein levels were either the same or less in hearts and lungs of nitrofen-exposed mice than in normal tissues except in pseudoglandular lungs. Different expressions of mRNA and protein suggest possible post-transcriptional or translational defects in Cx43. We observed dysmorphic hearts with exaggerated interventricular grooves and deep notches at the apex of the hearts in nitrofen-exposed fetal / neonatal mice; narrowed pulmonary out-flow and various degrees of craniofacial defects in 15-20% of the affected mice. Our data suggest a possible involvement of Cx43 in craniofacial, heart and lung defects in nitrofen-exposed mice. Such cardiopulmonary defects are also observed in human newborns with CDH. Thus, the murine data may help elucidate the pathways of cardiopulmonary defects in the human newborn condition.