Pre-treatment methamphetamine (MA) use frequency is an important predictor of outcomes of treatment for MA dependence. Preclinical studies suggest females self-administer more MA than males but few clinical studies have examined potential sex differences in MA use frequency. Estrogen increases expression of brain-derived neurotrophic factor (BDNF) which has effects on MA-induced striatal dopamine release and protects against MA-induced neurotoxicity. Therefore, we examined potential effects of sex, the Val66Met polymorphism in BDNF, and their interaction, on MA use frequency among 60 Caucasian MA dependent volunteers screening for a clinical trial. Females reported significantly more pre-treatment days with methamphetamine use in the past 30 than males. There was a significant interaction between sex and BDNF Val66Met with the highest frequency of MA use among females with Val/Val genotype. These results, although preliminary, add to the literature documenting sexual dimorphism in response to stimulants including methamphetamine and suggest a potential biological mechanism involving BDNF that may contribute to these differences. Additional research characterizing the biological basis of altered response to methamphetamine among females is warranted.