Heparin coating has recently been shown to reduce the risk of graft failure in arterial revascularisation, at least transiently. The aim of this study was to assess the cost-effectiveness of heparin coated versus standard polytetrafluoroethylene grafts for bypass surgery in peripheral artery disease from a long-term healthcare system perspective. Cost-effectiveness evaluation was conducted alongside the Danish part of the Scandinavian Propaten trial in which 431 patients planned for femoro-femoral or femoro-popliteal bypass surgery were randomised to either type of graft and followed for 5 years. Based on the intention to treat principle, the differences in healthcare costs (general practice, prescription medication, hospital admission, rehabilitation, and long-term care in 2015 Euros), life years (LYs), and quality adjusted life years (QALYs) were analysed as arithmetic means with bootstrapped 95% confidence intervals. Cost-effectiveness acceptability curves were used to illustrate the probability of cost-effectiveness for a range of threshold values of willingness to pay (WTP). No statistically significant differences between the randomisation groups were observed for costs or gains of LYs or QALYs. The average cost per QALY was estimated at €10,792. For a WTP threshold of €40,000 per QALY, the overall probability of cost-effectiveness was estimated at 62%, but owing to cost savings in patients with critical ischaemia (cost per QALY <€0), it increased to 89% for this subgroup. Until further evidence, heparin coated grafts appear overall, to be cost-effective over standard grafts, but important heterogeneity between claudication and critical ischaemia should be noted. While the optimal choice for claudication remains uncertain, heparin coated grafts should be used for critical ischaemia.