BackgroundSegmental bone transport is a common technique for treating large segmental bone defects. However, a docking site procedure is often necessary in segmental bone transport. To date, no prognostic factors for the need of docking site procedure have been reported. Thus, the decision is often made at random, based on the surgeon’s subjective judgment and experience. The aim of this study was to identify prognostic factors for the need of docking site operation.MethodsPatients with segmental bone transport in lower extremity bone defects were included regardless of age, aetiology, and defect size. We excluded patients undergoing treatments that were not yet completed, and those who discontinued therapy by any reason. The need for docking site operation was modelled with logistical and linear regression as well as univariate analysis of variances (ANOVA). Receiver operating characteristics (ROC) curve analysis was also performed.ResultsTwenty-seven patients from age 12 to 74 years (mean age: 39.07 ± 18.20 years) were included. The mean defect size was 76.39 ± 41.10 mm. The duration of transport (days) showed a significant influence (p = 0.049, 95%CI: 1.00–1.02) on the need for docking site operation. No other significant influences were detected.ConclusionA link between the duration of transport and the need for docking site operation was detected. Our data showed that if a threshold of about 188 days is exceeded, docking surgery should be considered.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12891-023-06593-6.