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Background Carriers of the E4 allele for the gene encoding apolipoprotein E (apoE) have an increased risk of atherosclerosis. The distribution of apoE genotypes among men with a small abdominal aortic aneurysm (AAA) was compared with that among healthy men, and any differences between the genotypes in aneurysm expansion measured over 2–4·5 years were examined. Methods The patients originate from a population ultrasonographic screening programme with about 4800 participating 65–73-year-old men in a defined geographical region. Of 191 patients diagnosed, 57 of 77 who have been followed for 2 years or more were genotyped. Aneurysm expansion rates were determined from linear regression of diameter versus time of examination. The influence of apoE genotype on expansion rate was analysed using analysis of variance, with initial aneurysm size and smoking status as covariates. Results The E4E4 genotype was not seen among patients with an AAA, whereas three patients had the rare E2E4 genotype. These patients had higher expansion rates than patients with the common genotype E3E3 (P = 0·009), whereas patients with the genotype E3E4 had lower rates (P = 0·034) (see Table over). Conclusion The findings suggest that the common polymorphism of the apoE gene influences the prognosis in patients with a small AAA. As regards the E3E4 genotype, the findings are unexpected, when compared with the known influence of E4 on the risk of atherosclerosis. This may partly explain the familial tendency of AAA, and inconsistent finding of coexisting atherosclerosis in patients with AAA. However, an impact of selection bias, due to differential survival or referral to surgery of patients with AAA, cannot be excluded.