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Introduction The aim was to study the effect of incisional negative pressure wound therapy (iNPWT) in wound healing compared with standard sterile gauze dressings after major lower extremity amputation in patients with peripheral arterial disease (PAD). Methods This prospective, randomised controlled trial included 50 patients undergoing major lower extremity amputations for PAD. Patients were randomised into iNPWT and standard dressing groups. The patency of blood vessels at the level of the stump was ensured with or without revascularisation. The primary outcome was wound-related complications such as surgical site infection (SSI), wound dehiscence, seroma/haematoma formation or the need for revision amputation. The secondary outcome was the time taken for the eligibility of prosthesis placement. Results It was found that only 12% of the patients in the iNPWT group had SSI compared with 36% in the standard dressing group (p = 0.047). Rates of wound dehiscence, seroma/haematoma formation and revision amputation were decreased in the iNPWT group but this was not statistically significant (p > 0.05). There was a significant reduction in the time taken for eligibility of prosthesis placement in the iNPWT group (5.12 ± 1.53 vs 6.8 ± 1.95 weeks, p = 0.002). Conclusions iNPWT is effective in reducing the incidence of SSI and the time taken for rehabilitation in patients undergoing major lower limb amputation due to PAD.