Due to improved efficacy of antitumour treatment in the general population, there are increasingly more childhood cancer survivors. However, some of these survivors are at risk of distant complications including cardiovascular disease. We aimed to examine the risk of overweight/obesity and abnormal body composition in a large group of patients from our paediatric oncology centre. We used anthropometric methods and electrical bioimpedance to assess these features, and then determined their association with disease and treatment. We found patients treated for leukaemia/lymphoma (especially boys) had significantly higher rates of overweight/obesity compared to the other patient groups. On the contrary, overweight/obesity was more common in girls among patients treated for solid tumours. Patients treated for leukaemia/lymphoma were characterised by a higher body fat content compared to those treated for solid tumours and controls. During treatment for cancer, patients had a higher percentage of muscle mass deficiency compared to those in the control group. Our regression analysis showed time from completion of treatment, gender and type of therapy (radiotherapy, megachemotherapy) were associated with body weight and body composition including fat and muscle content. We recommend paediatricians and general practitioners should actively try to detect and prevent cardiovascular disease among childhood cancer survivors.