Introduction: Cardiovascular diseases (CVD) are one of the long-term side effects of childhood cancer treatment. Salusin β is an indicator of atherosclerosis development. The aim of the study was to evaluate serum salusin β levels in long-term acute lymphoblastic leukaemia survivors (ALLs) and Wilms' tumour survivors (WTs) and compare these levels to established CVD risk factors. Material and methods: Thirty-seven ALLs and eleven WTs underwent physical examination and laboratory tests after an overnight fast at least 5 years after the end of oncological treatment. The laboratory tests included analysis of lipid profiles, serum glucose levels, renal parameters and salusin β levels. Results: The groups did not vary in age, time from the end of the treatment, number of obese persons, blood pressure, lipid profile, serum creatinine and glucose levels. The ALLs had greater weights and greater waist circumferences. The serum cystatin level was higher and the cystatin-based estimated glomerular filtration rate was lower in the WTs. Salusin β was higher in the WT group, but the result was not statistically significant. Conclusions: Acute lymphoblastic leukaemia survivors and WTs differ in terms of types of long-term side effects. Acute lymphoblastic leukaemia survivors more often develop obesity and metabolic problems, whereas WTs tend to develop renal disorders. Salusin β levels are associated with the level of LDL in ALLs and can indicate lipid disorders in patients with higher risk of obesity, suggesting that it could be a predictor of atherosclerosis. Further investigations are necessary to confirm this result. It is necessary to continue follow-up among adults who have been treated for childhood cancers to reveal long-term side effects such as cardiovascular disorders.