How does paying federal and state taxes work for an online business?

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The business will pay federal income taxes in the same way it would if it was a brick-and-mortar business.  The address for filing will be the principal business address of the entity.  Whether or not you will be required to pay state income taxes will depend on the laws of the particular states in which you transact business (i.e., in which your customers reside).  Also be aware that many states impose sales tax on items sold online to residents in the state.  You must review your business model with an attorney knowledgeable in these matters.

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