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Background Obsessive-compulsive disorder (OCD) is a highly prevalent and devastating psychiatric condition.Repetitive transcranial magnetic stimulation (rTMS) is a potential and non-invasive treatment for OCD.Diverse efficacies of rTMS have been reported in different locations or frequencies of the stimulation.The main objective of this study was to assess the treatment effect for OCD with alpha electroencephalogram (αEEG)-guided TMS over dorsal Iateral prefrontal cortex bilaterally.Methods There were 25 OCD patients in the αTMS treatment group and 21 OCD patients in the sham control group.Each subject received 10 daily treatment sessions (5 days a week).The αTMS group had significant reduction in scores of Yale-Brown Obsessive Compulsive Scale and Hamilton Rating Scale for Anxiety (HAMA) compared with the control group at the end of 2-week treatment and 1-week follow-up.Analysis of variance with repeated measures was used to test the effects between the two groups.Results Significant difference in scores of obsession and HAMA were found between the two groups after treatment.No significant difference in scores of Hamilton Rating Scale for Depression was found between the two groups after the treatment,but statistical significance was shown at the end of 1-week follow-up.Conclusions αEEG-guided TMS may be an effective treatment for OCD and related anxiety.Delayed response to αTMS in depression suggests that it might be secondary to the improvement of primary response in OCD and anxiety.