Background: Adolescents with intellectual disability (ID) (ID-adolescents) and adolescents with chronic diseases are both more likely to have emotional and behavioural problems. The aim of this study was to assess the association between chronic diseases in ID-adolescents and emotional and behavioural problems in a large school-based sample. Methods: We obtained data on 1044 ID-adolescents, aged 12-18 years, attending secondary schools in the Netherlands. Parents of the adolescents completed the Dutch version of the Strengths and Difficulties Questionnaire and questions about chronic diseases in their child and about the background of the child. Results: Prevalence rates of emotional and behavioural problems were generally high in ID-adolescents with chronic diseases (45%), compared with ID-adolescents without chronic diseases (17%). The likelihood of emotional and behavioural problems was high in ID-adolescents with two [odds ratios (OR) 4.47; 95% CI: 2.97-6.74] or more than two chronic diseases (OR 8.01; 95% CI: 5.18-12.39) and for ID-adolescents with mental chronic diseases (OR 4.56; 95% CI: 3.21-6.47). Also ID-adolescents with somatic chronic diseases had a high likelihood of emotional and behavioural problems (OR 1.99; 95% CI: 1.33-2.99), in particular in the combination of somatic and mental chronic diseases (OR 5.16; 95% CI: 3.46-7.71). Conclusions: The current study showed that chronic diseases in ID-adolescents, in particular mental chronic diseases, largely increase the likelihood of emotional and behavioural problems. This should be taken in the provision and planning of care for ID-adolescents.