In many intoxication-type inherited metabolic disorders, the accumulation of the toxic chemical can cause acute life-threatening emergencies. Sometimes this is the inevitable consequence of a severe metabolic defect, but it is often triggered by catabolism. In this article, we consider the acute management when these conditions cause encephalopathy, seizures, stroke-like episodes, thromboses, liver failure, cardiac failure, arrhythmias and rhabdomyolysis. Treatment is available for most intoxication-type disorders, though it is seldom entirely satisfactory. The emergency management involves general measures for the immediate problem (such as liver failure, thrombosis or an arrhythmia) and specific treatment for the metabolic disorder. The latter usually aims to reduce the accumulation of the toxic small molecule. Often this involves preventing or reversing catabolism. Sometimes the formation of the toxic chemical can be reduced by removing dietary precursors, by diverting precursors to alternative pathways, or by inhibiting an earlier step in the affected pathway. Another strategy is to remove the toxic chemical by binding it to a drug or by extracorporeal blood purification. Occasionally, the block in the pathway can be ameliorated and some disorders, specific treatment may prevent the consequences of the accumulating chemical. Despite all these treatment strategies, outcomes are often disappointing, particularly if an intoxication disorder first presents as an emergency. Newborn screening has greatly improved the prognosis for some disorders. For others, outcomes can only be improved by earlier recognition and treatment.