The role of computer-assisted surgery in maintaining the level of the joint in primary knee joint replacement (TKR) has not been well defined. We undertook a blinded randomised controlled trial comparing joint-line maintenance, functional outcomes, and quality-of-life outcomes between patients undergoing computer-assisted and conventional TKR. A total of 115 patients were randomised (computer-assisted, n = 55; conventional, n = 60). Two years post-operatively no significant correlation was found between computer-assisted and conventional surgery in terms of maintaining the joint line. Those TKRs where the joint line was depressed post-operatively improved the least in terms of functional scores. No difference was detected in terms of quality-of-life outcomes. Change in joint line was found to be related to change in alignment. Change in alignment significantly affects change in joint line and functional scores.