WHO defines malnutrition as severe if the z-scores are less than - 3 Standard deviation (SD), moderate if between - 2 and - 3 SD and mild if between - 2 SD to - 1 SD. This study was aimed to assess nutritional aspects of Indian children suffering from EB and to evaluate the effect of severity of EB on the severity of malnutrition. In this study, pediatric EB patients were evaluated prospectively for baseline nutritional status using anthropometric parameters and WHO growth charts, and its correlation with disease severity using instrument for Scoring Clinical Outcomes for Research of Epidermolysis Bullosa-iscorEB. In second phase, an individualized diet chart was given to meet the energy, protein and micronutrients needs and its effects were observed after 6 months. The median age of participants was 3 years (IQR-9). Of 57 patients, malnutrition was seen in 40.35% patients (22.81%-moderate and 17.54%-severe), and significantly correlated with iscorEB (r = 0.45, p < 0.0001). On bivariate regression analysis, iscorEB was independently associated with moderate-to-severe malnutrition (p = 0.047; OR 1.038, CI 1.011-1.066). iscorEB enabled the identification of patients with moderate-to-severe malnutrition with an Area Under Receiver Operating Curve (AUROC) of 0.72 (95%CI 0.58-0.85; p < 0.005). In phase 2, there was significant improvement in nutritional status in children with recessive dystrophic EB (RDEB) and dominant dystrophic EB (DDEB) subtype (p < 0.0001). The severity of malnutrition in EB children significantly correlates with disease severity, and is an independent predictor of moderate-to-severe malnutrition.