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The study aim was to evaluate the impact of body mass index (BMI) on disease progression over 2-years in 242 participants aged 3-20 years with Charcot-Marie-Tooth disease (CMT) enrolled in the Inherited Neuropathy Consortium (INC). BMI was classified using the International Obesity Task Force criteria (equivalent to an adult BMI): severely underweight (BMI<17kg/m2), underweight (BMI≥17kg/m2 to <18.5kg/m2), healthy weight (BMI≥18.5kg/m2 to <25kg/m2), overweight (BMI≥25 kg/m2 to <30 kg/m2); obese (BMI≥30kg/m2). Disease severity was assessed using the CMT Pediatric Scale (CMTPedS), a clinical outcome assessment of disability. At baseline, being severely underweight, underweight, or obese was more disabling than being a healthy weight (p<0.02). After 2-years, CMTPedS mean scores deteriorated by 0.9 (SD 5.1) to 2.3 (SD 5.4) points across BMI categories (p<0.0001), with the severely underweight patients progressing at the fastest rate. At 2-years, being severely underweight remained more disabling than being a healthy weight (p=0.02). Upon stratification, in the children who did not change BMI categories (69%), CMTPedS scores increased faster in children who were severely underweight (6.4 SD 3.2 points) than those of a healthy weight (1.8, SD 4.9 points, p<0.001). For the remaining 74 children (31%) who moved across BMI categories over 2-years, CMTPedS scores worsened in those children who changed categories to underweight or severely underweight (2.3, SD 5.4 points, p=0.082) or obese (2.8, SD 5.8 points, p=0.042). Children with CMT who are severely underweight had greater progression in disability over 2-years, than children who were healthy weight, overweight, or obese. Being severely underweight at baseline or moving to an unhealthier BMI category, results in worse disability at 2-years. BMI appears important in understanding the natural history of CMT and for prognostic enrichment of clinical trials. Interventions that maintain or improve BMI into a healthy range may result in decreased disability in children with CMT.