We previously compared the component alignment in total knee replacement using a computer-navigated technique with a conventional jig-based method. We randomly allocated 71 patients to undergo either computer-navigated or conventional replacement. An improved alignment was seen in the computer-navigated group. The patients were then followed up post-operatively for two years, using the Knee Society score, the Short Form-36 health survey, the Western Ontario and McMaster Universities osteoarthritis index, the Bartlett Patellar pain questionnaire and the Oxford knee score, to assess functional outcome. At two years post-operatively 60 patients were available for assessment, 30 in each group and 62 patients completed a postal survey. No patient in either group had undergone revision. All variables were analysed for differences between the groups either by Student's t-test or the Mann-Whitney U test. Differences between the two groups did not reach significance for any of the outcome measures at any time point. At two years postoperatively, the frequency of mild to severe anterior pain was not significantly different (p = 0.818), varying between 44% (14) for the computer-navigated group, and 47% (14) for the conventionally-replaced group. The Bartlett Patellar score and the Oxford knee score were also not significantly different (t-test p = 0.161 and p = 0.607, respectively). The clinical outcome of the patients with a computer-navigated knee replacement appears to be no different to that of a more conventional jig-based technique at two years post-operatively, despite the better alignment achieved with computer-navigated surgery.