The aim of the present study was to test for a possible association between two brain-derived neurotrophic factor (BDNF) polymorphisms (rs11030101 and rs61888800) and the efficacy of electroconvulsive therapy (ECT) [change in Montgomery–Åsberg Depression Rating Scale (MADRS)]. So far, there are no studies investigating an association between these polymorphisms and the efficacy of ECT. The patient sample included 119 patients with treatment-resistant major depressive disorder who were treated with ECT. BDNF polymorphism rs11030101, but not rs61888800, was associated with a change in the MADRS score. Patients with the TA genotype of rs11030101 were less likely to benefit from ECT compared with patients with the TT genotype (P=0.041). The finding suggests an association between BDNF polymorphism rs11030101 and the efficacy of ECT. Further studies with larger samples will be required to confirm this finding.