The repeated administration of 3,4-methylenedioxymethamphetamine (MDMA) produces neurotoxicity in the 5-hydroxytryptamine (5-HT) and dopamine systems of the brain. In this study, we investigated the effects of minocycline, a second-generation tetracycline derivative, on MDMA-induced neurotoxicity in the 5-HT and dopaminergic systems of the mouse brain. The repeated administration of MDMA (10 mg/kg × 3, 3-h intervals, s.c.) significantly decreased the contents of 5-HT and its major metabolite 5-hydroxyindole acetic acid (5-HIAA) in the frontal cortex and hippocampus, and the density of the 5-HT transporter (5-HTT) in the frontal cortex, hippocampus and striatum. The repeated administration of MDMA (10 mg/kg × 3, 3-h intervals, s.c.) significantly decreased the contents of the dopamine and the density of the dopamine transporter (DAT) in the striatum, but not the frontal cortex. Furthermore, pretreatment and the subsequent administration of minocycline (40 mg/kg, i.p.) significantly attenuated the reduction of 5-HT and dopamine as well as the density of 5-HTT and DAT in the mouse brain by the repeated administration of MDMA. Moreover, pretreatment and the subsequent administration of minocycline (40 mg/kg) significantly attenuated the increase of activated microglia in the hippocampus and striatum after the repeated administration of MDMA. Our findings suggest that minocycline protects the neurotoxicity of the 5-HT and dopamine systems in the mouse brain after the administration of MDMA.