In this study, we tested the hypothesis that diet composition reported by children before the beginning of an obesity treatment program could be a predicting factor of the clinical outcome. A sample of 138 obese 6–16-year-old children and adolescents were recruited. Anthropometry and dietary habits were recorded. Each patient participated in a multidimensional treatment program in an outpatient obesity public service clinic. Therapy was based on a 6-month educational program on nutrition, lifestyle and physical activity. Children with a lipid intake above 34.7% of total energy had a 2.5 times higher chance of reducing at least 1.5 units of BMI with treatment than children with lower lipid intake. These results suggest that the assessment of habitual diet, in particular diet composition before starting treatment, may help to identify obese children who are more sensitive to intervention and those who need more specific nutritional assistance.