Recently estimating the uncertainty of an analytical result has become an essential part of quantitative analysis. This study describes the uncertainty of the measurement for the determination of methamphetamine and its major metabolite amphetamine in human hair, The method consists of washing, drying, weighing, incubation and extraction with methanolic HCI solution, clean-up, trifluoroacetyl derivatization, and qualification/quantification of residues by gas chromatography/mass spectrometry (GC/MS). Traceability of measurement was established through traceable standards and calibrated volumetric equipment and measuring instruments. Measurement uncertainty associated with each analyte in real samples was estimated using quality control (QC) data. The main source of combined standard uncertainty comprised two components, which are uncertainties associated with calibration linearity and variations in QC, while those associated with preparation of analytical standards and sample weighing were not so important considering the degree of contribution. Relative combined standard uncertainties associated with the described method ranged for individual analytes from 4.99 to5.03%.