Background: In adolescents with intellectual disability, the management of obesity is a crucial issue, yet also quite complex because of their particular perception of themselves. This study investigated the relationship between self-perception variables and morphological variables and their changes after a 9-month Adapted Physical Activity (APA) programme. Materials and Methods: Twenty-three adolescents with intellectual disability responded to an adapted questionnaire, including the PSI-VSF-ID and a nine-drawing body silhouette scale. Anthropometric and body composition indicators were measured before and after the APA programme. Results: The main predictor of the adolescents' self-perceptions was the inclination towards positive illusory bias before the intervention; obesity awareness ranked second. Morphological measurements did not contribute in the same way to self-perceptions in the initial and final data. Conclusions: This study confirms the interest of weight management programmes for adolescents with intellectual disability and points to the need to take positive illusory bias more fully into account in the study of self-perception.