The possible associations between coronary heart disease (CHD) and peripheral arterial disease (PAD), detected by echo-Doppler analysis, with restriction fragment length polymorphism (RFLP) of apo AI/CIII cluster and apo B gene were investigated in a group of men with premature CHD (n = 39) and in a control group of men without evidence of CHD (n = 40). The genetic analysis of SstI RFLP of apo AI/CIII cluster showed a significantly higher frequency of the rare SstI allele (S2) in CHD patients (0.16) as compared with controls (0.06). No significant differences were found in the frequencies of XbaI RFLP for the apo B gene between CHD patients and controls. Moreover, patients with PAD showed no significant differences in the frequencies of XbaI RFLP for the apo B gene and of SstI RFLP for the apo AI/CIII cluster as compared with patients without evidence of peripheral arterial disease detected by echo-Doppler analysis.