The aim of this study was to assess the predictive value of lipoproteins and apolipoproteins at a young age for the development of coronary artery disease at middle and older ages. Because children of coronary artery disease patients are at high risk themselves we compared lipoprotein and apolipoprotein levels between the offspring of parents with and without coronary artery disease. We selected a group of male patients (n = 90), who had severe coronary atherosclerosis at angiography, and a reference group of male controls (n = 62), who had no coronary atherosclerosis at angiography. Lipoprotein and apolipoprotein levels were determined in 115 sons and 73 daughters of the patients with severe coronary atherosclerosis. These were compared to levels in 68 sons and 47 daughters of controls. Additionally, lipoprotein and apolipoprotein levels were compared between patients and controls as well as between their spouses. In sons of patients, lower levels of HDL3 cholesterol (-0.07 mmol/1, standard error of the mean (SEM) 0.03, P < 0.05) and apolipoprotein A2 (-5.1 mg/dl (SEM, 1.4), P < 0.0001) were found compared to sons of controls. Similar differences were observed in daughters of such patients without, however, achieving statistical significance. No significant differences between the groups of offspring were found for total cholesterol, LDL cholesterol, HDL and HDL2 cholesterol, triglycerides and apolipoproteins A-I and B. Patients had higher levels of total (group difference 0.6 mmol/1 (SEM, 0.18), P < 0.001) and LDL cholesterol (0.6 mmol/1 (SEM, 0.17), P < 0.001), triglycerides (0.6 mmol/1 (SEM, 0.16), P < 0.001) and apolipoprotein B (21.2 mg/dl (SEM, 5.1), P < 0.001), and lower HDL cholesterol (0.1 mmol/1 (SEM, 0.04), P < 0.05) than controls. Spouses of patients had higher levels of triglycerides (0.23 mmol/1 (SEM, 0.11), P < 0.05). Our findings add to the growing evidence that predictors for atherosclerotic disease can be detected relatively early in life. It is concluded that reduced levels of HDL3 cholesterol and apolipoprotein A2 may be early risk indicators for coronary atherosclerosis later in life.