Chronic kidney disease, characterized by gradual loss of renal function and irreversible progression, is becoming a major public health problem worldwide. Chronic kidney disease may lead to end-stage renal disease, as well as increase the morbidity and mortality associated with cardiovascular disease. This review focuses on identifying risk factors indicating the need for intervention in early stages of chronic kidney disease, as well as determining factors that may improve patient prognosis. However, all the risk factors giving rise to the progression of chronic kidney disease have not yet been identified. Metabonomics is a new type of omics that reflects the real-time pathophysiology of disease and focuses on endogenous metabolites of low molecular weight. This new and powerful tool has recently been used to explore metabonomic biomarkers of chronic kidney disease, enabling early diagnosis and timely intervention and treatment to slow the progression of chronic kidney disease. This review summarizes recent findings on the identification, using a metabonomic approach, of biomarkers associated with risk factors for the development and progression of chronic kidney disease.