Bone transport can be performed with an external fixator alone or with the monorail technique which entails the combination of a fixator and an intramedullary nail. The purpose of this study was to compare the complication rates and long-term outcomes of these methods. Two groups of patients, the external fixator (n = 21) and the monorail group (n = 18), were compared. The average follow-up period was 7.9 ± 5.6 years and the mean defect length 8.3 ± 3.1 cm. Healing was achieved in 19 (90%) and 13 (72%) of the fixator and monorail patients, respectively. Six patients underwent amputations because of persistent infections (two in the fixator and four in the monorail group). The rate of deformities was significantly higher in the fixator group (p = 0.049). No statistically significant difference was found when comparing categories of the SF-36 test or the ability to work or do sports. The main advantages of the monorail method are reduction of the external fixation time and the lower rate of deformities. However, the authors recommend segmental transport with external fixator in patients with chronic infections.