Is the audit risk any different if I file the 1040 or if a CPA files the (same) 1040?

The IRS isn't helpful here, as they will not say one way or 'tother.

In my own opinion, it probably makes no difference unless the PTIN or EFIN on the return has been somehow flagged as a suspect preparer or ERO.

There is no way to know for sure and the IRS won't tell. I can tell you what I THINK but I have to confess that part of that is tied to my professional ego. I think the gives more credence to professionally prepared return WHEN the return is complicated, and the more complicated the return the better I think your audit chances are when a licensed pro signs off on it. I think this is the case because they taxing agencies know that the tax laws are complex and most Americans have difficulty with the returns that have more complex issues.

BUT I don't know that, fact certain, and I can't prove it. And I can't define "complex" because the returns I do are complex for my clients but not so much for me (with 30-years in the biz).

Gene E. Utterback, EA, RFC, ABA

Regarding your posting subject line, I personally would recommend an EA over a CPA, because with the former you are selecting a someone who is licensed directly by the IRS to prepare taxes and represent taxpayers, while with the latter you are selecting an accounting professional, certified by a state board, who may or may not have expertise with taxes.

In fact, the OP's premise is faulty, in that most tax pro's would not just blindly e-file a self-prepared return without exercising due diligence with respect to the items reported on the return. If indeed there is a bias in favor of returns signed by paid preparers, that is almost certainly the reason. After all, the paid preparer who signs is putting themselves on the line for penalties and sanctions beyond those the taxpayer is subject to -- so, to put it plainly, would you be more likely to trust a document that two unrelated people (one a professional) have signed under penalties of perjury, or just one person (not a professional)?

As mentioned earlier, however, this cuts both ways. The unethical and fraudulent tax preparers, hopefully very few in number and dwindling (as new paid preparer registration requirements kick in), can actually increase the audit risk of their clients. When deciding whether and which preparer to choose, use your common sense, the use of which, for once, is not precluded by tax law.