Each of the 30 to 40 inborn errors of amino acid and or organic acid metabolism represent a rare occurrence in perinatal medicine. However, their combined incidence is about 1/4000 in the neonatal period. Their importance derives from what they tell us about intermediary metabolism and from the fact that these are generally treatable diseases if detected early. This chapter discusses the development of selected amino acid enzymes, pathways of amino acid and organic acid catabolism, and specific aminoacidopathies and organic acidurias that present in the neonatal period. These disorders include the organic acidemias such as propionic acidemia, methylmalonic acidemia, glutaric acidemia type II, multiple carboxylase deficiency, the urea cycle disorders, maple syrup urine disease, and nonketotic hyperglycinemia. The focus is on the biochemistry of these disorders, approaches to treatment and outcome (see Chapter 53).