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Your institution affiliation will display on the Interfolio cover sheet that accompanies every delivery you send out through the system.
If you are applying to medical school, your affiliation is generally your undergraduate institution.
If you are a Ph.D. or graduate student, your affiliation will generally be the school from which you received, or expect to receive, your degree.
If your school has a partnership with Interfolio, affiliating with that institution will also give them access to your documents.
If you wish to make your file private, you can do this in the "Account Settings" section of your account.
If you do not see your school or department listed, you can choose "My School is Not Listed" or "No Affiliation." You will not be able to change your affiliation through your account, but you can always contact Interfolio Customer Service to update it.