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The application and evaluation of highly efficient chromatographic techniques with tandem mass spectrometry for the detection and quantitation of 108 pesticides and metabolites, some considered persistent organic pollutants, was performed in muscle samples obtained from 25 birds of prey belonging to the families Accipitridae, Falconidae, and Strigidae presented dead in 2013 to Grupo de Rehabilitación de la Fauna Autóctona y su Hábitat, in Madrid, Spain. Pesticides with prohibited use were detected at high concentrations in the muscle samples analyzed. Based on its high sensitivity to detect pesticides in muscle, the described chromatographic techniques with tandem mass spectrometry should be considered an alternative testing methodology to those commonly used for routine application in ecotoxicological forensic research.