Abstract Adults with intellectual disabilities (IDs) have poor lifestyle-related health compared with the general population. Our aim was to study whether such differences are present already in adolescents. Aim: To compare the prevalence and severity of cardio-metabolic risk factors and cardio-vascular fitness in adolescents with and without IDs. Methods: Intellectual disability (ID) students (n = 66) and non-intellectual disability (non-ID) students from practical (non-ID-p) (n = 34) and theoretical (non-ID-t) (n = 56) programmes were recruited from three upper secondary schools. Anthropometric data, blood pressure, body composition, fasting-insulin, fasting-glucose, fasting-lipids and cardio-vascular fitness were measured. Results: Participants with and without ID differed significantly in the prevalence of cardio-metabolic risk factors with participants with ID having a higher percentage of total fat mass, wider waist circumferences (WCs), lower levels of fat-free mass (FFM), lower bone mineral density (BMD) and higher insulin and homeostasis model assessment of insulin resistance (HOMA) levels and poorer cardio-vascular fitness. The healthiest levels were found in the non-ID-t group compared to the group with ID and the group with non-ID-p in between. Conclusion: The prevalence of cardio-metabolic risk factors and poor cardio-vascular fitness was found to be high in this young population with intellectual disabilities. Measures should be taken to improve the health messages directed towards children and adolescents with intellectual disabilities.