We describe the use of hair roots as a matrix for detection of methamphetamine (MP) and 3,4-methylenedioxymethamphetamine (MDMA) abuse. The concentration of drugs was determined in rat hair roots, hair shafts, and plasma after a single administration of MP or MDMA, by use of an HPLC-peroxyoxalate chemiluminescence (PO-CL) method involving column switching. Plasma and hair roots and shafts were collected from male Wistar rats before and after administration of MP (10 mg kg(-1), i.p.). In addition, the roots and shafts of pigmented and non-pigmented hair of male Lister hooded rats were collected after administration of MDMA (10 mg kg(-1), i.p.). The concentrations of MP and MDMA in plasma and hair were determined by use of the HPLC-PO-CL method, with satisfactory sensitivity and reproducibility. The concentration of MP in hair roots 1-14 days after administration ranged from 0.038 to 0.115 ng mg(-1) (n = 3). By use of the HPLC-PO-CL method, MP could be detected in hair roots for longer (up to 14 days) than it could be detected in conventional biological specimens, for example plasma (~1 day), and MDMA was detected in hair roots from 1 to 10 days after administration. The AUC(1-10) (ng day mg(-1)) for MDMA in roots of non-pigmented and pigmented hair was comparable (4.93 ± 2.09 vs. 6.67 ± 1.28, n = 3), whereas AUC(1-14) for hair shafts differed significantly (1.86 ± 0.93 vs. 4.58 ± 0.63, P < 0.05, n = 3). The window for detecting MP (or MDMA) in hair roots under our conditions was 1-14 (or 1-10) days.