Maternal diabetes and obesity are independent risk factors for neural tube defects, although it is unclear whether the effects are mediated by common pathogenic mechanisms. In this manuscript, we report a genome-wide survey of histone acetylation in neurulation stage embryos from mouse pregnancies with different metabolic conditions: maternal diabetes, and maternal consumption of a high fat content diet. We find that maternal diabetes, and independently, exposure to high-fat diet, are associated with increases and decreases of H3 and H4 histone acetylation in the embryo. Intriguingly, changes of H3K27 acetylation marks are significantly enriched near genes known to cause neural tube defects in mouse mutants. These data suggest that epigenetic changes in response to diet and metabolic condition may contribute to increased risk for neural tube defects in diabetic and obese pregnancies. Importantly, the responses to high-fat diet and maternal diabetes were distinct, suggesting that perturbed embryonic development under these conditions is mediated by different molecular pathways. This conclusion is supported by morphometric analyses that reveal a trend for maternal diabetes to delay embryonic development in the C57BL/6 strain, while high-fat diet appears to be associated with accelerated development. Taken together, our results link changes in histone acetylation to metabolic conditions during pregnancy, and implicate distinct epigenetic mechanisms in susceptibility to neural tube defects under conditions of maternal diabetes and obesity. Birth Defects Research (Part A) 2012. © 2012 Wiley Periodicals, Inc.