Aims The Ilizarov bone transport (BT) technique is a common surgical method for treating segmental bone defects. However, major issues with the BT technique are prolonged external fixation period and docking site problems. This study aims to introduce a new modification of the Ilizarov technique – shortening and in situ relengthening (SISRL) – specifically for treating bone defects in the metaphyseal long bones in the lower limbs, and to compare its effectiveness with that of BT technique. Methods This retrospective comparative study included 70 patients with segmental bone defects in the lower limbs following direct trauma or osteomyelitis debridement, treated between January 2019 and January 2021. Patients were divided into two groups based on the Ilizarov technique used: the SISRL group (n = 32) and the BT group (n = 38). Data on bone lengthening time, external fixation time (EFT), and external fixation index (EFI) were collected. Pain from pin-track skin damage during the distraction period was assessed using a visual analogue scale (VAS). Bone and functional outcomes, the function of adjacent joints, and complications were all collected and evaluated. Results SISRL was associated with a significant reduction in mean EFT (220.8 days (SD 71.8) vs 278.4 days (SD 79.4); p < 0.001) and mean EFI (39.0 days/cm (SD 6.2) vs 46.5 days/cm (SD 6.6); p < 0.001). The SISRL group required fewer interventions. During the distraction phase, SISRL patients experienced less median pain (VAS 5.6 (IQR 5.2 to 6.5) vs 7.3 (IQR 6.9 to 8.1); p < 0.001) . SISRL patients had better functional results (p = 0.011) and joint functional scores (p < 0.001) compared to the BT group. Conclusion Compared with BT, SISRL was associated with reduced EFT, EFI, and patients’ pain during the distraction phase. Due to lengthening occurring at the location of the bone defect, SISRL was associated with better preservation of the adjacent joint function and avoidance of problems at the docking site. It showed superior clinical results with metaphyseal segmental defect of lower limb long bones after trauma and infection. Cite this article: Bone Joint J 2025;107-B(12):1343–1351.