We are scanning our paperwork right now, however I am not sure if pdf files are acceptable for audits. Is there any rule on when and if originals can be destroyed?

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Electronic records are acceptable and original paper documents may be destroyed. Please see the IRS Revenue Procedure 98-25.

It's important to note that if you retain paper documents along with electronic copies, the paper documents control, i.e. you have to supply the paper documents in an audit. However, making electronic versions of the documents and destroying the paper is acceptable provided that you follow the rules set forth in IRS RP 98-25.

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