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Background: There is a lack of prospective studies with popliteal aneurysms (PAA) < 2 cm and the very few information about the natural cause of the disease. Patients and methods: Between 1995 and 2000 46 patients having 65 popliteal artery aneurysms have been examined. The mean diameter was 1.9 cm (0.8–4 cm). In 41% of the cases PAA were bilateral, additional extrapopliteal aneurysms were found in 37%. The PAA was occluded in 8 patients at the initial examination (mean diameter 2.4 cm: 1.4–4 cm). One of these patients had to be amputated (long-term diabetes, dialysis and severe generalized peripheral arteriosclerosis). Since no information could be obtained from two patients, it was possible to prospectively monitor 36 patients with 46 PAA (30 m, 6 f) over a period of 2.5 years. 19 patients were treated with platelet inhibitors, 16 with coumarin and one refused any thromboembolic prophylaxis. The patients were examinated every year by telefone interview and duplexsonography. Results: During the monitoring period there occurred two complete occlusions and one distal arterial progression, while 2 patients died, but no amputation. The total complication rate was 6.5% with a higher incidence in PAA > 2 cm of diameter (14.2 vs. 3.1 %). All complications were found in PAA with mural thromboses. Coumarin seems to be superior platelet aggregation inhibitors with a complication rate of 0% vs. 14.3%. The mean increase in diameter during follow-up was dependent on PAA size, 1.5 mm/year for PAA > 2 cm vs. 0.7 mm/year for PAA < 2 cm. Conclusion: This prospective study emphasises the necessity of a prophylactical surgery in patients with an aneurysm diameter > 2 cm. In view of the low rate of complications of the natural course of PAA (6.5% of all PAA or 14.2% for PAA > 2 cm/2.5 years), the bypass surgery should be performed by an experienced vascular department. Patients with PAA < 2 cm or patients with contraindication for peripheral bypass should receive anticoagulation.