Inherited metabolic disorders account for a small but significant number of sudden unexplained deaths in neonates, infants and occasionally older children. In particular, inherited disorders of fatty acid oxidation may closely mimic sudden infant death syndrome. Post-mortem investigations offer the final opportunity to establish a diagnosis. Such diagnoses are of great importance to the families concerned and provide the opportunity for genetic counselling and antenatal diagnosis. Current advances in technology, particularly in the case of electrospray ionization tandem mass spectrometry, have revolutionized the investigation of metabolic disease at post-mortem, facilitating the identification of a wide range of metabolic diseases in tiny samples of blood, plasma and bile. Such analyses may provide vital clues to diagnosis, usually in the form of acylcarnitine profiles. Accurate diagnosis relies on the timely collection of appropriate samples and the subsequent selection of informative testing. In order to maximize the chances of a diagnosis, a collaborative approach between the various disciplines is vital. A brief description of the more frequently encountered inherited disorders, collection and processing of appropriate samples and available investigations that may lead to accurate diagnosis are clearly described.