This study will examine the effects of rTMS on the negative and positive symptoms of schizophrenia using 2 treatments in sequence applied to related brain areas.

Inclusion Criteria:

1. are voluntary and competent to consent to treatment
2. have a diagnosis of schizophrenia or schizoaffective disorder
3. are between the ages of 18 and 75
4. are willing and able to adhere to the treatment schedule
5. Pass the TMS adult safety-screening (TASS) questionnaire
6. have normal thyroid functioning based on pre-study blood work. Patients may be reassessed for the study once thyroid levels have normalized.
7. are willing and able to cooperate with interviews and follow simple instructions

Exclusion Criteria:

1. do not pass the TASS Safety Screening Questionnaire
2. have a significant history of seizures
3. have active suicidal intent
4. are pregnant or may be pregnant. A pregnancy test will be performed for fertile women.
5. have failed a course of Electroconvulsive Therapy (ECT) in the current or previous episode
6. have any significant neurological disorder or insult including, but not limited to: any condition likely to be associated with increased intracranial pressure, space occupying brain lesion, any history of seizure except those therapeutically induced by ECT, cerebral aneurysm, Parkinson's disease, Huntington's chorea, multiple sclerosis, or head trauma resulting in loss of consciousness greater than or equal to 5 minutes
7. have an intracranial implant (e.g., aneurysm clips, shunts, stimulators, cochlear implants, or electrodes) or any other metal object within or near the head, excluding the mouth, that cannot be safely removed
8. have had changes in dose or initiation of any psychotropic medication in the 4 weeks prior to screening. Patients may be re-screened once medications have been stable for 4 weeks.
9. currently (or in the last 4 weeks) take more than lorazepam 2 mg daily (or equivalent) or any dose of an anticonvulsant due to the potential to limit rTMS efficacy