Purpose: To present our treatment protocol and surgical outcome for patients with congenital brachymetatarsia in which treatment was decided according to the number of affected rays. Materials and Methods: Sixty-nine metatarsals in 44 patients with single or multiple congenital brachymetatarsia were included in the study. When a single ray was affected in a foot, we performed a one-stage lengthening using an intercalary autogenous iliac bone graft. We overcame excessively short rays by the double level lengthening at the metatarsal and proximal phalanx as one stage. When multiple rays were affected in one foot, we performed a one-stage combined shortening and lengthening procedure without an iliac bone graft. Results: All patients were satisfied with the cosmetic and functional results. The average length gain by one-stage lengthening in 56 metatarsals of 38 patients was 14 (6-21) mm. Six patients with a combined shortening and lengthening procedure regained a nearly normal parabola of the involved foot. Neurovascular complication was not identified. Conclusion: Satisfactory results were achieved for the treatment of patients with congenital brachymetatarsia, by individualizing the surgical options according to the number of affected rays and general foot appearance.