The nutritional cues which induce different phenotypes from a single genotype in developing offspring are poorly understood. How well prenatal nutrient availability before birth predicts that after birth may also determine the offspring's response to later metabolic challenge. We investigated the effect of feeding pregnant rats diets containing protein at 180 g/kg (Control) or 90 g/kg (protein-restricted, PR) and either 1 or 5 mg folic acid/kg on growth and metabolic response to fasting in their offspring, and also the effect of diets with different fat contents (40 g/kg (Fat(4)) or 100 g/kg (Fat(10))) after weaning. Offspring of dams fed the PR diet with 5 mg/kg folic acid were significantly lighter than other offspring. The PR offspring fed the Fat(4) diet had lower plasma TAG than the Control offspring, but this relationship was reversed when offspring were fed Fat(10). Increasing the folic acid content of the Control or PR maternal diets induced opposing effects on plasma TAG, NEFA, beta-hydroxybutyrate and glucose concentrations in offspring fed Fat(4). The effect was accentuated in offspring fed the Fat(10) diet such that these metabolites were increased in the Control offspring, but reduced in the PR offspring. These data show for the first time that maternal dietary folic acid intake alters offspring phenotype depending upon dietary protein intake, and that this effect is modified by fat intake after weaning. Prevention by increased folic acid intake of an altered metabolic phenotype by maternal protein-restriction may be at the expense of somatic growth.