Low HDL concentrations are considered an important risk factor for cardiovascular disease. Interventions promoting a low-fat, plant-based eating pattern appear to reduce CVD risk while paradoxically also reducing HDL concentrations. Recent studies show HDL to comprise a range of subfractions, but the role these play in ameliorating the risk of CVD is unclear. The purpose of this study was to characterise changes in HDL subfractions in participants where HDL decreased following the CHIP intervention which promotes a low-fat, plant-based diet, with physical activity.