independent faces a lot of audits. You can expect at least one a year. If you are the PIC or if your PIC is also your lazy boss, then it will fall on you to keep everything in order.
The smaller one is a desktop audit. Typically it comes from the insurance companies themselves. They give you a rx number and a date of service and want you to fax them the front and back of your prescription along with the patient's signature for that date of service. Then in a couple months they will let you know if there is any discrepancies and how much the chargeback will be. This is typically triggered because you submitted a claim with an unusual quantity and day supply- for example 3 bottles of lantus for 30 days- and their computer flags it. Caremark likes to do this.
The bigger one is in-pharmacy audit (*** hits the fan time). The third party payer will hire an audit company to come to your place. They will send you a notice on what date they will be there and how far back they will look at your record (typically two years). They won't tell you what specific prescriptions they come to look at. Typically they are after expensive items. They don't care if you miss a drug interaction and kill someone. They just want to take everything back so hang on to your underwear.
When the person is there, he or she will give you a list of all the rxs they need. You need all your hard copy rxs in order (they don't care what you scan into your system). You need your signature logs. You need to make sure your day supply is calculated correctly, origin codes, written date, doctor's npi etc.. all correct. Just the fact that your origin code is wrong (e.g., rx was a verbal order and someone keyed it in as a fax), you will stand to lose all of your reimbursement on every single fill of that prescription.
So those are the little things that you have to pay attention to everyday, not just around the time of the audit. Many pharmacists I know tend to miss out on them because they rely on the techs to get it right, but if your techs suck at typing then it will fall back on you.