Objectives To evaluate the primary patency rate at three years for the infra-aortic peripheral arterial pathologies treated with polytetrafluoroethylene-covered stent-grafts. Methods Patients treated with self-expandable polytetrafluoroethylene-covered stent-grafts for infra-aortic peripheral arterial aneurysms, pseudo-aneurysms, and arterio-venous fistulas were evaluated retrospectively. A total of 48 patients (35 male, 13 female; mean age: 53.8 ± 13.5) were included with 29.0 ± 16.5 months (median 27, range 4–70) mean follow-up period. The primary objective was to determine the primary patency rate at three years. The secondary objectives were to compare type and localization of pathology, and length and diameter of the stent-grafts with primary patency rate. Kaplan–Meier test was used as the main statistical method. Results Overall mean primary patency rate at three years was 77.10%. Polytetrafluoroethylene-covered stent-graft implantation in aneurysms had worse primary patency rate than pseudo-aneurysms and arterio-venous fistulas (66.6%, P = 0.03; 76.9%, P = 0.03; 88.2%, P = 0.01, respectively). Stent-graft location, length, and diameter are not associated with primary patency rate ( P > 0.05) but stent diameter is associated with better primary assisted and secondary patency rates ( P < 0.05). Conclusions Pathology of the lesion is associated with the long-term primary patency rate of polytetrafluoroethylene-covered stent-grafts but not the stent-graft location, length, or diameter. Stent diameter is associated with primary assisted and secondary patency rates.