Oesophageal atresia/Tracheo-oesophageal fistula (OA/TOF) are common congenital malformations of the foregut in newborns. Until recently little was known about the pathogenesis of these anomalies. Adriamycin, a chemotherapy agent, has been found to cause birth defects in mice that resemble the OA/TOF anomalies providing an animal model to study the etiology of the defects. A number of genes have been implicated in regulating normal development of the trachea and oesophagus where mutations in mice cause abnormal development. This project examines the possible involvement of such candidate genes in the Adriamycin-treated mouse model. Optical projection tomography (OPT) is a 3D imaging technique that allows visualisation of gene expression patterns in the anatomical context of the embryo allowing changes in gene expression to be related to alterations in morphological events. Genes involved in cell communication systems integral to lung and foregut development are been examined in this way. Time-mated CBA/Ca mice received intraperitoneal injections of adriamycin (6 mg/kg) or saline on day 7 and 8 of gestation. Embryos were harvested on days 9–12 and stained following whole mount insitu hybridization with labeled RNA probes to detect specific gene transcripts. Immunohistochemistry using an antibody specific to endoderm cells (Hnf3b) was used to visualize morphology. Among the genes under analysis is Tbx4 a member of the forkhead family of transcription factors involved in spatial patterning of mesoderm differentiation. The temperospatial expression of Tbx4 during the critical period of separation of the trachea and oesophagus in normal and adriamycin treated embryos was revealed.