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Abstract Background Fibular hemimelia has been reported as the most common congenital longitudinal deficiency of the long bones. Previous studies have focused on the best treatment options for this congenital condition. There is very little to our knowledge in the literature focused on residual persisting malformations and leg length discrepancy after treatment. Methods Seven patients presenting fibular hemimelia in eight fibulae received treatment between years 1988 and 2001. Pre-treatment average leg length discrepancy was 5.3 cm. All patients presented associated congenital deformities of the ipsilateral leg. Six patients received surgical treatment. Average post-treatment follow up was 9.7 years. Residual malformations and leg length discrepancy were recorded for all patients. It is a retrospective case series study at one institution by two of the presenting authors as senior surgeons. Results Average leg length gained after successful bone lengthening in six patients was 5.06 cm. Although there was a significant functional improvement, a number of residual malformations and leg length inequality was recorded. Residual average leg length discrepancy of 3.1 cm was observed in five patients who completed surgical treatment. Five patients presented a limp. Residual anterior-medial bowing of the tibia was observed in four patients. Calf atrophy was present in all seven patients. Valgus deformity of the ankle was remained in two patients. Conclusions Treatment of fibular hemimelia, even in cases graded as successful, showed to be accompanied by a number of persisting residual deformities and recurrent leg length inequality. Although the number of patients is limited, the high rate of this phenomenon is indicative of the significance of the report. The family and the patients themselves should have the right expectations and will be more co-operative when well informed about this instance. A report of common post-treatment residual deformities should be valuable in best possible treatment planning of fibular hemimelia.