OBJECTIVE: Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) is increasingly used in newborn screening programs. Acylcarnitine profiles from dried blood spots (DBS) are used to detect fatty acid oxidation disorders, carnitine cycle disorders, and organic acidurias. Stored dried blood is also a valuable source for postmortem investigations to unravel the cause of unexplained death in early childhood. However, diagnostic uncertainties arising from the unknown stability of acylcarnitines and free carnitine during prolonged storage have not yet been studied in a systematic manner. METHODS: Whole blood spiked with acylcarnitines was stored either at -18 degrees C or at room temperature up to 1000 days. At regular time intervals 3.2 mm spots of these samples were extracted with 150 microL of methanol. Free carnitine and acylcarnitines were converted to their corresponding butyl esters and analyzed by ESI-MS/MS. RESULTS: At -18 degrees C acylcarnitines are stable for at least 330 days. If stored for prolonged periods at room temperature (>14 days), acylcarnitines are hydrolyzed to free carnitine and the corresponding fatty acids. The velocity of decay is logarithmic and depends on the chain length of the acylcarnitines. Short-chain acylcarnitines hydrolyze quicker than long-chain acylcarnitines. CONCLUSION: The data indicate that stored filter cards should only be used for retrospective quantitation of acylcarnitines if appropriate correction for sample decay during storage is applied. Free carnitine increases upon storage but can reliably be quantitated under standardized derivatization conditions. Furthermore, carnitine transporter (OCTN2) deficiency can reliably be diagnosed by examining acylcarnitine profiles, which can supplement free carnitine levels as a discriminatory marker.