Amphetamine-type stimulants (ATS), synthetic cathinones (SCs) and phenethylamines (PEAs) pose a challenge to toxicology laboratories. Their extensive use and misuse has led to an increase of intoxications and fatal incidents worldwide. So, the need for new analytical methods for their determination in biological samples is crucial for all toxicology laboratories for a better investigation of these cases. The aim of this study was the development and validation of an analytical method for the determination of 9 ATS, 7 SCs and 5 PEAs in whole blood and urine using gas chromatography coupled with mass spectrometry. The samples were pretreated by solid-phase extraction and derivatized with pentafluoropropionic anhydride. Chromatographic separation of the 21 analytes was achieved in less than 11 min. The method was validated according to international guidelines for selectivity, specificity, linearity, limits of detection (LODs) and quantification (LOQs), precision, accuracy and recovery of the method. The LODs of the analytes ranged from 0.70 to 7.0 ng/mL and the values of the LOQs ranged from 2.0 to 20 ng/mL. The linearity of the 21 analytes, according to the group of substances, were 2.0 ng/mL - 0.20 μg/mL, 5.0 ng/mL - 0.50 μg/mL, 10 ng/mL - 0.50 μg/mL and 20 ng/mL - 0.50 μg/mL with R2 values > 0.99. Extraction recoveries were > 80 % for all analytes. Intra and inter day accuracy and precision of the method were within accepted limits. The developed method was applied to post-mortem blood and urine samples of 46 forensic cases sent for toxicological investigation to the Department of Forensic Medicine and Toxicology, School of Medicine, National and Kapodistrian University of Athens. The results of the analyses revealed the presence of methamphetamine, amphetamine, MDMA, MDA, pseudoephedrine, phenylpropanolamine or MBDB in 14 cases.