Introduction Repair of a bone defect in primary total knee arthroplasty remains one of the most common tasks that must be addressed intraoperatively. Autologous bone grafting is a good biological option to preserve the bone tissue for conservative revision. The objective of the study was to analyze the results of autologous bone grafting of the medial tibial defect in primary total knee arthroplasty. Material and methods Results of autografting a bone defect with cancellous bone obtained when forming a groove for the intercondylar box of the femoral component of the tibia during primary total knee arthroplasty were retrospectively analyzed (main group, n = 31). The control group (n = 31) was formed by leveling the heterogeneous clinical parameters identified in the initial data using the PSM method. The mean follow-up period was 72 months. The Mann-Whitney and Wilcoxon tests were used for statistical data analysis. Lower limb realignment and bone graft reconstruction were evaluated radiographically, and KSS and WOMAC questionnaires were used for physical evaluation. Results There were no significant differences in the baseline and postoperative clinical conditions of the realigned lower limbs and the number of identified non-progressive radiolucent lines no greater than 2 mm in the groups. There were significant differences in the severity of varus deformity at baseline. Each group had one case of aseptic loosening of the tibial component. One patient of the comparison group had a late periprosthetic joint infection that was arrested with two-stage revision treatment. Discussion There were significant differences in the size of the varus deformity with no significant differences in the scores at the baseline between the groups. There were no differences in the realigned lower limbs and in the scores reported in the groups postoperatively. Conclusion The method developed was shown to be safe, affordable and effective. The result obtained was confirmed by absent differences in clinical and radiological outcomes between groups.