Repetitive transcranial magnetic stimulation (rTMS) is a painless and safe brain stimulation technique that has been found to be effective in treating depression symptoms. The potential usefulness of rTMS, in particular to treat drug resistant patients, might be increased by identifying genetic predictors of efficacy. According to this rationale, we investigated the role of two functional polymorphisms in the genes coding for the serotonin transporter (5-HTTLPR) and the brain-derived neurotrophic factor (BDNF Val66Met), and rTMS response in a group of 36 drug resistant patients affected by mood disorders. rTMS treatment significantly improved depression symptomatology (p<0.0001) and the response was significantly greater in 5-HTTLPR LL homozygotes compared to S allele carriers (p=0.007) and in BDNF Val/Val homozygotes compared to Met allele carriers (p=0.024). These findings provide evidences about the involvement of both polymorphisms in rTMS antidepressant response. Further investigations in larger samples are needed to clarify the usefulness of 5-HTTLPR and BDNF Val66Met genotyping in the optimization of non-pharmacological treatments in mood disorders.