Diabetes during pregnancy is associated with aortic remodelling in the fetus, stimulating the development of cardiovascular diseases in adult life. However, studies suggest that the use of foods high in omega-3 fatty acid, such as flaxseed oil, may reverse this effect of metabolic programming. This study aimed at investigating whether the effects of diabetes in mothers are passed on to their offspring in a gender-specific manner and whether the flaxseed oil used during pregnancy and lactation reverses or not the possible negative effects of this programming. Diabetic female rats (n = 18) were mated and allocated into three groups (n = 6): high-fat group (HG); flaxseed oil group (FOG) and control group (CG) (nondiabetic rats) during pregnancy and lactation. On the 21st day, male and female pups were weaned on a standard diet until 180 days. Aorta histomorphometry was analysed. Intima-media layer thickness was larger in FOG than CG in male (+15%) and than HG in female (+13.7%). Male FOG (+11.5%) showed higher amount of elastic fibre than CG. Maternal intake of flaxseed oil during pregnancy and lactation of diabetic mothers program the offspring to increase aorta intima-media layer thickness in adulthood and preserves aorta elastic fibres deposition in male offspring.