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We report the efficacy of three versus single session of 10 Hz repetitive transcranial magnetic stimulation (rTMS) in chronic migraine (CM) and chronic tension-type headache (CTTH). Ninety-eight patients with CM or CTTH were included and their headache frequency, severity, functional disability and number of abortive medications were noted. Fifty-two patients were randomly assigned to group I (three true sessions) and 46 to group II (one true and two sham rTMS sessions) treatment. 10 Hz rTMS comprising 600 pulses was delivered in 412.4 s on the left frontal cortex. Outcomes were noted at 1, 2 and 3 months. The primary outcome was 50 % reduction in headache frequency, and secondary outcomes were improvement in severity, functional disability, abortive drugs and side effects. The baseline headache characteristics were similar between the two groups. Follow up at different time points revealed significant improvement in headache frequency, severity, functional disability and number of abortive drugs compared to baseline in both group I and group II patients, although these parameters were not different between the two groups. In group I, 31 (79.4 %) had reduction of headache frequency and 29 (74.4 %) converted to episodic headache. In group II, these were 24 (64.8 %) and 22 (59.2 %), respectively. In chronic migraine, the severity of headache at 2 months reduced in group I compared to group II (62.5 vs 35.3 %; P = 0.01). Both single and three sessions of 10 Hz rTMS were found to be equally effective in CM and CTTH, and resulted in conversion of chronic to episodic headache in 67.1 % patients.