Twenty patients underwent simultaneous bilateral medial unicompartmental knee arthroplasty. Pre-operative hip-knee-ankle alignment and valgus stress radiographs were used to plan the desired post-operative alignment of the limb in accordance with established principles for unicompartmental arthroplasty. In each patient the planned alignment was the same for both knees. Overall, the mean planned post-operative alignment was to 2.3 degrees of varus (0 degrees to 5 degrees ). The side and starting order of surgery were randomised, using conventional instrumentation for one knee and computer-assisted surgery for the opposite side. The mean variation between the pre-operative plan and the achieved correction in the navigated and the non-navigated limb was 0.9 degrees (sd 1.1; 0 degrees to 4 degrees ) and 2.8 degrees (sd 1.4; 1 degrees to 7 degrees ), respectively. Using the Wilcoxon signed rank test, we found the difference in variation statistically significant (p < 0.001). Assessment of lower limb alignment in the non-navigated group revealed that 12 (60%) were within +/- 2 degrees of the pre-operative plan, compared to 17 (87%) of the navigated cases.Computer-assisted surgery significantly improves the post-operative alignment of medial unicompartmental knee arthroplasty compared to conventional techniques in patients undergoing bilateral simultaneous arthroplasty. Improved alignment after arthroplasty is associated with better function and increased longevity.