Growing evidence supports the hypothesis that the in utero environment can have profound implications for fetal development and for offspring health in later life. Current theory suggests that conditions experienced in utero prepare, or ‘programme’, the fetus for its anticipated post-natal environment. The mechanisms responsible for these programming events are poorly understood but are likely to involve gene expression changes. Folate is essential for normal fetal development and inadequate maternal folate supply during pregnancy has long term adverse effects on the offspring. We tested the hypothesis that inadequate folate supply during pregnancy alters offspring programming through altered gene expression. Female C57BL/6J mice were fed diets containing 2 mg folic acid/kg or 0.4 mg folic acid/kg for 4 weeks before mating and throughout pregnancy. At 17.5 day gestation, genome-wide gene expression in fetal liver and placenta of male offspring was measured by microarray analysis. In the fetal liver, 989 genes (555 up-regulated, 434 down-regulated) were expressed differentially in response to maternal folate depletion, with 460 genes expressed differentially (250 up-regulated, 255 down-regulated) in the placenta. Only 25 differentially expressed genes were common between organs, revealing that maternal folate intake during pregnancy influences fetal gene expression in a highly organ specific manner which, we propose, reflects prioritised protection of essential organ-specific functions.