Aminoacidopathies and organoacidopathies are the most common acute life-threatening inborn errors of metabolism in the neonatal period. In the Federal Republic of Germany approximately 1 out of 5000 newborns is currently diagnosed as having an aminoacidopathy and approximately 1 out of 9000 newborns an organoacidopathy. Especially in the case of organoacidopathies there is substantial evidence that this number represents an underestimation. Many cases of amino- and organoacidopathies are still likely to remain undiagnosed. The incidence figures would warrant neonatal population screening for these disorders; however, the complexity and expense of the current methods prohibit this approach. Instead specialized investigations are carried out in children who develop symptoms indicative of an inborn error of metabolism. This approach is called selective screening. Early diagnosis, therefore, rests on a high degree of suspicion. In this paper clinical and laboratory findings of amino- and organoacidopathies are summarized. They can be nonspecific and misinterpreted. In the neonate and infant the presentation is commonly that of an acute overwhelming disease, whereas in the older child unexplained mental and/or neurological problems are often the leading symptom. We present an algorithm for the quick and comprehensive diagnosis of acutely presenting inborn errors of metabolism using commonly available parameters. However, in many cases the definitive diagnosis is not reached by selective metabolic screening of a single urine specimen of a patient, but requires close cooperation between the referring physician and the metabolic specialist. Multiple analyses, sometimes of different physiological fluids, or even in vivo and in vitro loading tests may be necessary.(ABSTRACT TRUNCATED AT 250 WORDS)