Objective: To explore the independent associations of body height, body mass index (BMI), waist circumference and hip circumference with high-density lipoprotein-cholesterol (HDL-cholesterol) and non-high-density lipoprotein-cholesterol (non-HDL-cholesterol), in a large general population sample. Design: Cross sectional. Setting: Urban and rural areas throughout Greece. Subjects: In total, 10 837 volunteers, 2034 men and 8803 women, aged 25-82 years, participants in the European Prospective Investigation into Cancer and Nutrition study (EPIC), who have never smoked and never been treated for dyslipidemia. Interventions: None. Results: The effect of height on non-HDL-cholesterol was opposite but in absolute terms almost as important as that of BMI with no gender interaction. Among women, hip circumference was inversely associated with non-HDL-cholesterol (standardized coefficient b st = -1.11, with standard error (s.e.) = 0.42) and positively with HDL-cholesterol (b st = -0.85, s.e. = 0.12) whereas, waist circumference was inversely associated with HDL-cholesterol (b st = -1.16, s.e. = 0.13) and strongly positively with non-HDL-cholesterol (b st = 8.83, s.e. = 0.45). Among men, associations were generally weaker (in absolute terms by about 50%) and for hip circumference the association with non-HDL-cholesterol was actually non significantly positive. Conclusions: Height was inversely associated with HDL and non-HDL-cholesterol implicating early life phenomena in the regulation of these variables. Larger hip circumference among women had beneficial effects on blood cholesterol fractions by increasing HDL-cholesterol and reducing non-HDL-cholesterol, whereas among men the relevant effects were less clear cut. The detrimental consequences of large waist circumference on both HDL (reduction) and non-HDL-cholesterol (increase) were also particularly marked among women.