Purpose Recurrent genu valgum deformity complicates treatment of congenital femoral deficiencies (CFD) and fibular hemimelia (FH). We analysed factors influencing recurrence. Methods Patients who underwent limb lengthening or deformity correction for CFD and/or FH were reviewed. Radiographs after surgery and after a minimum of a further six months were analysed. Change in parameters of mechanical axis deviation per month (Δ MAD/month) and of angle per month were calculated. These parameters were tested against cofactors patient age, baseline MAD, type of CFD and FH, severity of ball-and-socket joints, ankle-joint stiffness, absence of cruciate ligaments and resection of the fibular anlage. Results Recurrent valgus deformity was found in 23 of the 42 limbs included with a mean change of MAD of 23.4 mm (5-60 mm). There was no significant difference between patients with Δ MAD/month <0.5 mm versus >1 mm regarding MAD in the first radiograph and patient age. CFD cases Pappas types VII and VIII showed a Δ MAD/month of 1.6 mm, whereas milder cases of Pappas IX showed a Δ MAD/month of 0.8. Mild FH (type Ia) showed a mean Δ MAD/month of 0.39 mm, whereas mean Δ MAD/month for FH type Ib/II was 0.72 mm. In FH type II cases, mean Δ MAD/month was 0.79 mm after resection of the fibular anlage compared with 1.98 mm in those without resection.Conclusions Recurrence in FH and CFD was not dependent on patient age but partly on FH and CFD type. Limbs with more severe ball-and-socket knee joints showed more recurrence. Overcorrection depending deformity type should be performed.