Electroconvulsive therapy has a long history in the treatment of depression and its benefits are well known. Repetitive transcranial magnetic stimulation has been introduced more recently to the treatment spectrum. We tested the hypothesis that rTMS would be more efficient in the treatment of depression due to its equivalence in antidepressant effect and relatively more benign side effect profile, in comparison with ECT. Aims: To test the equivalence of rTMS with ECT, and compare the neurocognitive side effects of both treatment modalities. Methods: We conducted a non-randomized comparative study; forty patients with major depression referred for ECT were assigned in a consecutively alternating fashion to either a 20 session course of rTMS to the left dorsolateral prefrontal cortex or a standard course of ECT. The primary outcome measure was the score on the Hamilton Depression Rating Scale. Secondary outcome measures were a cognitive battery that assessed different aspects of cognitive functions and a subjective mood visual analogue scale. The cognitive battery comprised the Rey-Osterrieth complex figure test, the Trail making test A and B, the Digit span subtest from the Wechsler Adult Intelligence Scale, and the Stroop test. Results: ECT was substantially more effective than rTMS in the short-term treatment of major depressive disorder. This was evident from the end of treatment HAM-D scores differences between both groups (p=0.001, significant), and the response rate (in the ECT group N=10, in the rTMS group N=2, Fisher’s exact test, p=0.004). In those patients who responded to either treatment modality, the depth of the clinical response, was similar in both groups (p=0.519, non-significant). rTMS was well tolerated with less impact on the cognitive functions compared to ECT. In the ECT Group, the level of improvement correlated with severe baseline HAM-D symptoms. In the rTMS group the level of improvement correlated with more memory affection at the end of treatment and more severe baseline HAM-D symptoms. Conclusions: ECT was substantially more effective than rTMS in the short-term treatment of major depressive disorder. rTMS was well tolerated with less impact on the cognitive functions compared to ECT.