Non-alcoholic fatty liver disease (NAFLD) is characterised by low circulating concentration of high-density lipoprotein cholesterol (HDL-C) and raised triacylglycerol (TAG). Exercise reduces hepatic fat content, improves insulin resistance and increases clearance of very-low density lipoprotein-1 (VLDL1). However, the effect of exercise on TAG and HDL-C metabolism is unknown. We randomised male participants to 16 weeks of supervised, moderate-intensity aerobic exercise (n=15) or conventional lifestyle advice (n=12). Apolipoprotein A-I (apoA-I) and VLDL-TAG and apolipoprotein B (apoB) kinetics were investigated using stable isotopes (1-13C-leucine and 1,1,2,3,3-2H5 glycerol) pre and post intervention. Participants underwent MRI/spectroscopy to assess changes in visceral fat. Results are mean ± standard deviation.At baseline, there were no differences between exercise and control groups for age (52.4±7.5 vs 52.8±10.3 years), BMI (31.6±3.2 vs 31.7±3.6 kg/m2) and waist circumference (109.3±7.5 vs 110.0±13.6 cm). Percentage liver fat was 23.8 (interquartile range 9.8-32.5%). Exercise reduced body weight (101.3±10.2 to 97.9±12.2 kg; P<0.001) and hepatic fat content (from 19.6%, IQR 14.6-36.1% to 8.9% (4.4-17.8%); P=0.001) and increased the fraction HDL-C concentration (measured following ultracentrifugation) and apoA-I pool size with no change in the control group. However, plasma and VLDL1 TAG concentrations and HDL-apoA-I fractional catabolic rate (FCR) and production rate (PR) did not change significantly with exercise. Both at baseline (all participants), and after exercise, there was an inverse correlation between apoA-I pool size and VLDL TAG and apoB pool size. The modest effect of exercise on HDL metabolism may be explained by the lack of effect on plasma and VLDL1 TAG.