There is ample evidence that both diabetes as well as obesity leads to various metabolic disturbances that leads to oxidative stress. Oxidative stress has been shown to be associated with congenital malformations of which neural tube defects and cardiac malformations are more common. The cellular and molecular mechanisms through which oxidative stress induces these defects during the developmental stage are not well known. Previous work in this field suggests that oxidative stress results in lipid peroxidation and altered expression of genes that have key roles in the developmental processes. The present study aimed to investigate gene alterations in embryos from pregnant diabetic or obese rats. Embryos and adipose tissue obtained from the locally bred diabetic and obese Sprague-Dawley inbred rat strain were subjected to Total RNA extraction and were quantified using Real time PCR for relative gene expressions analysis. The present study showed that maternal diabetes as well as obesity diminishes the antioxidative defense mechanisms by down regulating the gene expressions of the key reactive oxygen species scavenging enzymes copper zinc superoxide dismutase and manganese superoxide dismutase in day 10 rat embryos. There was also altered embryonic gene expression for several developmental genes due to maternal diabetes at gestational day 11 and 13 in rat embryos.