The associations of apolipoprotein B (apoB) gene polymorphisms with blood lipid levels, also accounting for apo E polymorphisms, were assessed in 82 phenylketonuric (PKU) children on diet (34 girls, 48 boys, age 4-12 years, median 8 years). Dietary and plasma biochemical assessments were performed at six-month intervals from the age of 24 months onwards. Apo B (XbaI, MspI, EcoRI restricton sites) and apo E (E2, E3, E4) gene polymorphisms were determined by restriction-enzyme analysis after DNA extraction from blood. Subgroups of apoB polymorphisms were similar for energy intake, dietary lipids and distribution of apo E polymorphisms. Children carrying XbaI X+/X+ showed higher plasma levels of LDL cholesterol than children carrying X-/X-/+. This gene-related response to dietary habits might play a role also in non-PKU individuals fed low-fat, low-cholesterol diets.