PURPOSE: There remains controversy as to whether computer-navigated total knee replacement (TKR) improves the overall prosthesis alignment and patient function. The aim of this study was to determine whether computer-assisted total knee arthroplasty provides superior prosthesis positioning when compared to a conventional jig-assisted total knee replacement and whether this affected the functional outcome. METHODS: This prospective, randomised controlled study compared computer navigated and conventional jig-assisted total knee replacement in 37 patients who underwent bilateral TKR. A quantitative assessment of the spatial positioning of the implant in the 74 total knee replacements was determined using a low-dose dual-beam CT scanning technique. This resulted in six parameters of alignment that were compared. Functional outcomes using the high activity arthroplasty score and Knee Society score were assessed pre-operatively, postoperatively, at three years and at five years. Patients also indicated which knee they felt was subjectively the best. RESULTS: There was no statistically significant difference in the prosthesis alignment between both groups and the number of outliers was not decreased with navigation. All function scores improved from pre-operative to postoperative but there was no statistically significant difference between the groups at five years. At five years, 40.6% of patients thought their jig-assisted knee was the better knee compared with 21.9% their computer assisted knee and 37.5% of patients who felt they were the same. CONCLUSION: Computer-assisted implantation of total knee replacements does not offer a significant advantage in prosthesis alignment. There was no difference in functional outcome or subjective "best knee" between the computer-assisted or jig-assisted knee.