Knee anomalies are common in patients with congenital short femurs who require lengthening to correct limb-length discrepancies. We retrospectively reviewed the incidence of knee arthritis and the factors influencing its occurrence after femoral lengthening using the Wagner method. Twenty-three patients with congenital short femurs treated with the Wagner method were followed up until skeletal maturity (minimum, 5 years postoperatively). The mean age of the patients at lengthening was 10.8 years (range, 8.4-14.5 years). The mean leg-length discrepancy at the time of surgery was 9.7 cm (femur, 7.6 +/- 3.7 cm; tibia, 2.1 +/- 1.8 cm). Femoral lengthening (mean, 7.9 cm) was performed in 17 patients. Femoral lengthening and tibial lengthening were performed simultaneously in six patents (mean, 11.8 cm). The mean age of the patients at the last followup was 16.8 years (range, 14-20.3 years). Eighteen patients had arthritis at followup. Nine patients had severe arthritis develop, seven of whom had knee instability preoperatively and temporary subluxation during the lengthening procedure. Seventy-eight percent of patients had arthritis develop in the knee after lower-limb lengthening using the Wagner method for congenital short femurs. Patients who had an unstable knee before surgery had temporary knee subluxation develop during the lengthening procedure, and patients who had simultaneous lengthening of the femur and tibia had a high association with degenerative arthritis changes in the knee.