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The available comparative studies of computer navigation-assisted and conventional knee arthroplasties have short-term follow-up periods. Therefore, the clinical benefits after long-term follow-up are not clear. The purposes of the current long-term study were to compare clinical outcomes, alignment of the knee components, prevalence of aseptic loosening of the components, implant survival, and complications of total knee arthroplasties performed with and without computer navigation.We prospectively compared the results of 162 consecutive patients (324 knees) with osteoarthritis. These patients had computer-navigated knee arthroplasty in 1 knee and knee arthroplasty without computer navigation in the other. Nine men and 153 women were enrolled in the study. At the time of the index arthroplasty, the mean age of these patients was 68.1 years (range, 49 to 81 years). The mean duration of follow-up was 12.3 years (range, 12 to 13 years). Clinical and radiographic follow-up examinations of the patients were performed at 3 months, 1 year after the operation, and every 2 or 3 years thereafter.The Knee Society knee score, Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score, and range of knee motion were not significantly different between the groups preoperatively or at 12.3 years of follow-up. Patient satisfaction at the final follow-up was not significantly different between the groups. There were no significant differences between the groups with respect to the position and loosening of the components at 12.3 years of follow-up. The Kaplan-Meier survivorship, with revision or loosening as the end point, was 100% (95% confidence interval [CI], 94% to 100%) at 12.3 years in both groups. The prevalence of anterior femoral notching was higher in the computer-navigated knee arthroplasty group (5%) than in the conventional knee arthroplasty group (0.6%).Clinical function, position, and survivorship of the components were similar between the groups. The only effect of navigation was a negative one, anterior femoral notching. However, comparison of bilateral total knee arthroplasties may dampen the differentiation regarding pain outcomes. Further, the findings of this study are specific to a single navigation and total knee system.Therapeutic Level I. See Instructions for Authors for a complete description of levels of evidence.