Objective Computer-assisted surgery application in total knee arthroplasty (TKA) has shown more accurate implant alignment compared with conventional instrumentation and is associated with more homogeneous alignment results. Although longer implant survival and superior clinical outcomes should be expected from navigated TKA, currently available evidence does not support this hypothesis. The aim of this study was to compare navigated TKA with conventional TKA regarding clinical and radiological outcomes after a 3-year follow-up under the hypothesis that navigated TKA would provide better outcomes than conventional TKA. Material and method In a prospective multicentre study, 119 patients underwent navigated TKA and 80 patients received conventional instrumentation. Patients were evaluated at the baseline and at postoperative months 3, 12, 24, and 36. Analysis included the American Knee Society Score (KSS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Short Form-12 (SF12) Health Survey, and radiographic assessment. Results All clinical scores improved significantly for all patients during the follow-up but were significantly better in the navigation group. The percentage of patients showing a mechanical axis between 3° of varus and 3° of valgus was significantly higher in the ATR group (93%) than in the conventional TKA group (71%) (p Conclusions The use of computer-assisted surgery in TKA provides more accurate mechanical alignment and superior short-term functional outcomes compared to conventional TKA.