End-stage renal disease, the most severe form of chronic kidney disease (CKD), is a devastating disorder with mortality rates at least 30 times higher than that of age-matched peers. Children with less severe forms of CKD also suffer from lower quality of life, more disabilities, and more comorbidities than healthy children. Protein energy wasting (PEW) plays a central role in CKD. Multiple metabolic derangements such as retention of nitrogenous waste products and other uremic toxins, fluid overload, inflammation, endocrine disturbances, anemia, and metabolic acidosis collude in PEW's emergence. In addition, inadequate nutrition is common among patients with renal failure. Finally, dialysis contributes to the poor nutritional status as it causes losses of various micronutrients and alters protein and energy metabolism resulting in negative protein balance and increased energy expenditure. In this chapter, various applications of stable isotope techniques in pediatric renal disease are addressed. First, the assessment of total body water is discussed, as the major body of stable isotope research in the field of renal disease is dedicated to this subject. Also methods for the assessment of intra- and extracellular body water compartments are discussed. Second, studies into whole-body protein kinetics in CKD are addressed. The application of various stable isotope and chromatography techniques for the measurement of metabolism and losses of proteins and other substrates during dialysis treatment is then discussed. Finally, stable isotope studies in primary hyperoxaluria, a rare metabolic disorder affecting the kidneys, are addressed.