This study was designed to compare the qualitative results and concentrations of methamphetamine (MA) and its metabolite amphetamine (AP) in head hair and hair collected from different parts of the body (axillae and pubis). Hair from subjects (N = 14) suspected MA users was simultaneously collected. Hair preparation involved washing step, fine cutting, overnight extraction, derivatization by the trifluoroacetic anhydride, and gas chromatography/mass spectrometry (GC/MS) using selective ion monitoring. In this study, we found a good correlation of the qualitative results for MA between head hair and hair on other parts of the body, but there were some differences in concentrations of MA and AP. Namely, the concentrations of MA and AP were higher in axillary and pubic hair than in head hair.