Background: Childhood obesity has become a global pandemic and is one of the strongest risk factors for cardiovascular disease later in life. The correlation of epigenetic marks with obesity and related traits is being elucidated. This review summarizes the latest research and its challenges in the study of epigenetics of (childhood) obesity. Summary: Epigenome-wide association studies helped identify novel targets and methylation sites that are important in the pathophysiology of obesity. In the future, such sites will become essential for developing methylation risk scores (MRS) for metabolic and cardiovascular diseases. Although MRS are very promising for predicting the individual risk of obesity, the implementation of MRS is challenging and has not been introduced into clinical practice so far. Key Messages: Future research will undoubtedly discover numerous methylation sites that may be involved in the development of obesity and its comorbidities, especially at a young age. This will contribute to a better understanding of the complex etiology of human obesity. From a clinical perspective, the overarching aim was to generate MRS that is robust for reliable and accurate prediction of obesity and its comorbidities.