This chapter addresses the clinicopathologic features of kidney diseases in various categories of inherited metabolic diseases or inborn errors of metabolism, most often secondary to a systemic disease in the pediatric population. Considering the rarity of these diseases, renal involvement may be silent, purely functional and/or manifest parenchymal alterations with organ dysfunction. They may affect the glomerular, tubulo-interstitial or rarely vascular compartments, although they are not mutually exclusive in a given disease. The major groups of diseases include various forms of lipid, protein/lipoprotein, glycogen disorders and other organic substances, as a result of specific cellular organelle dysfunction or an inherited enzyme deficiency, allowing for accumulation of abnormal metabolites or substrates that cells are unable to eliminate effectively. The clinical manifestations may appear during the neonatal period or develop later during childhood with progressive organ dysfunction with a wide spectrum of signs and symptoms, having an acute, subacute or chronic presentation. The age of onset and disease severity may depend on the inheritance patterns and the type of gene mutations, as well as environmental influences. A detailed family history and genetic studies are often useful, along with clinical and laboratory findings at the time of presentation, to make a definitive diagnosis. Although the kidney is rarely a target organ, when affected, a renal biopsy is valuable in establishing a diagnosis and also in further delineating specific entities, based on their unique clinical, pathological, histochemical, ultrastructural and molecular/genetic characteristics.