Background: This study aimed to evaluate the clinical and functional outcomes of patients with critical femoral and tibial bone defects treated by trifocal bone transport using the Ilizarov method.Methods: In a retrospective comparative study, 39 patients treated for lower limb bone non-union with bone loss measuring between 6 and 14 cm were included. Depending on the location of bone transport, the patients were divided into the femur group (n =18) and tibia groups (n =21). The demographics data, intraoperative records, and postoperative outcomes were documented and compared between the two groups. At the last follow-up, the bone and functional outcomes were evaluated according to the criterion given by the Association for the Study and Application of the Method of the Ilizarov (ASAMI) and postoperative complications evaluated by Paley classification.Results: The average follow-up time was 26.1 months (range 17–34 months) since the unilateral external fixators were removed. The mean size of the bone defect was 8.3 cm in the femur group, and 7.5 cm in the tibia group. All bone defects were reconstructed successfully. The mean time in external fixation in the femur group was 334.4 days, and in the tibia group was 344.6 days. The external fixation index (EFI) measured 55.9 days/cm in the femur group and 65 days/cm in the tibia group. A statistically significant difference of bone grade was found between the two groups (excellent/good/fair/poor, 3/11/3/1 vs 2/13/4/2, P<0.05), as well as the function grade in two groups (excellent/good/fair/poor/failure, 3/14/1/0 vs 4/13/3/1, P<0.05). According to the ASAMI classification, the clinical and functional results in the femur group were better than in the tibia group. The complication rate of the two groups was 94.4% vs 76.2% (femur vs tibia). One femur and five tibias were performed additional surgery because of delayed union and axial deviation. Conclusions: The trifocal bone transport using the unilateral external fixator is a reliable treatment in the management of post-traumatic and post-infection lower limb bone defects (>6cm). In the comparison of the tibia, the trifocal bone transport treatment period of the femur was shorter, the functional recovery was better and the risk of minor complications was higher.