To assess whether there is a differential hypocholesterolemic response to weight loss for subjects carrying polymorphisms of the apolipoprotein B and other genes. A before and after comparison of lipid parameters following a calorie controlled diet for an intervention period of 12 weeks. A lipid clinic based in a large teaching hospital. The difference in slope coefficients relating the percentage change in lipid parameters to the change in body weight (adjusted for age, gender and initial body mass index (BMI)), for genotype subgroups defined by polymorphisms of the 5'VNTR apoB gene, two mutations of the LPL gene and ApoE. One hundred and forty six subjects completed the intervention diet. While, on average, the intervention was successful (mean weight loss 3.9%), there was no statistically significant difference in the slope coefficients relating lipid change to weight loss for most of the genotypes tested. The slope difference for long versus short 5'VNTR alleles of the apoB gene was 0.445 (-1.307, 2.198) for apolipoprotein B and -0. 104 (-1.486, 1.278) for total cholesterol. However, subjects carrying at least one varepsilon4 allele were significantly hypo-responsive to weight loss, difference in slope coefficients -1.087 (-2.09, -0.084) and -1.320 (-2.589, 0.051) for total cholesterol and apoB, respectively. Although, this study is one of the largest of its kind, it has not replicated the findings of other smaller studies. These findings do not provide support for the use of genotype-targeted dietary advice in routine practice.