The determination of selected short-, medium- and long-chain acylcarnitines by electrospray ionization mass spectrometry (ESI-MS) is discussed. The differences in fragmentation behaviour and ionization efficiency are described in dependence on collision induced dissociation (CID) conditions and mixture composition. A new method combination, solid-phase microextraction (SPME)-ESI-MS, is introduced to characterize acylcarnitines in body fluids. This method utilizes SPME for pre-concentration of acylcarnitines from complex biological samples and ESI-MS for a selective and sensitive detection. The method is presented by standard experiments determining of acylcarnitines in aqueous solutions and urine samples from patients with secondary carnitine deficiency syndromes or related disorders.