Acylcarnitine profiling in dried blood spots (DBS) is a useful method for high-throughput newborn screening of metabolic disorders, but differentiation of isobaric and isomeric compounds is not achievable. Chromatographic methods for separation have already been reported but are specific for short-chain acylcarnitines or time-consuming. The aim of this work was to develop a fast ultraperformance liquid chromatography (UPLC)-tandem mass spectrometry (MS/MS) method for separation and quantification of a large number of acylcarnitines, including dicarboxylic acylcarnitines and hydroxyacylcarnitines, in DBS and plasma samples. Acylcarnitines from DBS and plasma were converted to their butyl esters and analyzed by electrospray ionization MS/MS. Chromatographic separation was achieved using a UPLC system equipped with an ethylene-bridged hybrid C(18) column. The correlation coefficients of the calibration curves (r(2)) ranged from 0.990 to 0.999. The limit of detection ranged from 0.002 and 0.063 μM for all compounds, and the limit of quantification ranged from 0.004 and 0.357 μM. Precision ranged from 0.8 to 8.8% and the mean recovery was 103%. Profiles of acylcarnitine isomers were investigated in specimens obtained from patients diagnosed with different inborn errors of metabolism. Acylcarnitine concentrations were also measured in 58 term newborns and compared with flow injection analysis measurements. With this newly developed UPLC-MS/MS method, the simultaneous detection of 61 (13 of these labeled) acylcarnitines in DBS and plasma can be achieved in 15 min including postrun equilibration. The method has been validated and can be used as an important component of newborn screening methods as a second-tier test for discrimination and to confirm diagnosis.