Background: Computer Navigation in Total Knee Replacement (TKR) has completed more than a decade since its inception. From that time, numerous studies have been done to see its effect on the variables of surgery and its outcome. Some studies have shown that it is definitely beneficial while others have negated its superiority over conventional techniques. This is an early outcome study on the results of navigation TKR in terms of alignment and clinical outcome at three years post-operatively. Methods: In the present study, 128 patients who had undergone navigation TKR (128 TKR) between January 2006 and November 2009 were included. The navigation system used was orthoPilot . Patients were assessed post-operatively at one and three year using knee society score (KSS) and knee function score (KFS). All patients completed one year follow-up and 55 patients completed three year follow-up. From 128 patients, 40 navigated TKR patients operated between November 2007 and 2009 and were compared with 40 patients operated by conventional TKR operated between July 2007 and December 2008. Results: The mean KSS at 1 year post-operatively was 85.60 and at 3 years was 85.87. The mean KFS at 1 year post-operatively was 69.30 and at 3 years was 68.00. There was no statistically significant difference between navigation TKR and conventional TKR in terms of anatomical femoro-tibial alignment, femoral component alignment in coronal and sagittal plane and tibial component alignment in coronal plane. However, there was statistically significant difference between tibial component alignment in sagittal plane (p = 0.000) between both the groups. Conclusion: Computer navigation TKR affords a possibility to place both the femoral and tibial component very precisely without the risk of any greater axis deviation from ideal value. It helps in reducing the outliers in alignment of the limb and that of component and that improves the overall implant survival for a long time post-operatively.