If a payee indicates on the W-9 that they are a Limited Liability Company, and then write in that it is a disregarded entity, are we to send a 1099 to them?

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Yes, an LLC that is a disregarded entity is subject to 1099 reporting, if the amount paid is $600 or more.

Only if an LLC indicates that it is an S- or C-corp would it be exempt from reporting. 

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