The unique composition of green kiwifruit has the potential to benefit CVD risk. The aim of the present study was to investigate the effect of consuming two green kiwifruits daily in conjunction with a healthy diet on plasma lipids and other metabolic markers and to examine response according to APOE genotype in hypercholesterolaemic men. After undergoing a 4-week healthy diet, eighty-five hypercholesterolaemic men (LDL-cholesterol (LDL-C) > 3.0 mmol/l and TAG < 3 mmol/l) completed an 8-week randomised controlled cross-over study of two 4-week intervention sequences of two green kiwifruits per d plus healthy diet (intervention) or healthy diet alone (control). Anthropometric measures, blood pressure (BP) and fasting blood samples (plasma lipids, serum apoA1 and apoB, insulin, glucose, high-sensitivity C-reactive protein (hs-CRP)) were taken at baseline, and at 4 and 8 weeks. After the kiwifruit intervention, plasma HDL-cholesterol (HDL-C) concentrations were significantly higher (mean difference 0.04; 95% CI 0.01, 0.07 mmol/l; P = 0.004) and the total cholesterol (TC):HDL-C ratio was significantly lower (mean difference 20.5; 95% CI 20.24, 20.05 mmol/l; P = 0.002) compared with the control. In carriers of the APOE4 allele, TAG decreased significantly (mean difference -0.18; 95% CI -0.34, -0.02 mol/l; P = 0.03) with kiwifruit compared with control. There were no significant differences between the two interventions for plasma TC, LDL-C, insulin, glucose, hs-CRP and BP. The small but significant increase in HDL-C and decrease in TC:HDL-C ratio and TAG (in APOE4 carriers) suggest that the regular inclusion of green kiwifruit as part of a healthy diet may be beneficial in improving the lipid profiles of men with high cholesterol.