Inclusion Criteria:

• Male and female outpatients aged 18-55 years old
• Meet DSM-IV criteria for Bipolar Affective Disorder Type II, depressed phase without psychosis as determined by Structured Clinical Interview for DSM-IV
• A MADRS ≥ 15 at Initial Visit, and at Prior to TMS Evaluation
• A Young Mania Rating Scale < 12 at Initial Visit and at Prior to TMS Evaluation
• Duration of current episode of depression >2 months but ≤ 1 year of unsuccessful treatment
• On stable medication and/or psychotherapy for 1 month and clinically appropriate to maintain for duration of trial
• Cognitively intact (Folstein MMSE score >24).
• Clinically competent to give informed written consent

Exclusion Criteria:

• History of epilepsy or seizure disorder, mass brain lesions, cerebrovascular accident, metal in the skull, a history of major head trauma, or any neurologic condition likely to increase risk of rTMS.
• Suicidal risk that precludes safe participation defined as score of 5 or 6 on MADRS item 10 Suicidal Thoughts or clinical impression that the subject is at significant risk for suicide.
• History of any DSM-IV Axis I diagnosis other than Bipolar Affective Disorder Type II, depressed phase, simple phobia and generalized anxiety disorder (GAD) in the last year
• Lifetime history of schizophrenia, schizoaffective, or other psychotic disorder, bipolar disorder type I, dementia, dissociative disorders, and sexual and gender identity disorder
• Personality disorder that makes participation in the trial difficult
• Greater than or equal to 8 episodes of mood disturbance in the previous 12 months
• Greater than 4 unsuccessful treatments in current episode
• History of Substance Abuse or Dependence (DSM-IV) in the last year except nicotine and caffeine
• Positive urine drug test during screening
• Taking any medication that significantly lowers the seizure threshold (e.g. lithium, stimulants, bupropion, TCAs, antipsychotics, theophylline, etc.)
• Unstable medical conditions that precludes safe participation in rTMS treatment trial
• Known or suspected pregnancy
• Women of child-bearing potential not using medically accepted form of contraception when engaged in sexual intercourse
• Any metal or device implants that would increase risk of rTMS
• Unable to determine the motor threshold in the subject
• History of Vagus Nerve Stimulation
• Currently in another investigational study
• Prior electroconvulsive therapy failure