I wouldn't say don't count them - it's not like they don't count for something. They just shouldn't influence your overall code selection all that much. I mean, even with 9+ elements of ROS, you STILL have to have enough HPI and PFSH documented to qualify for a EPF, Detailed, or Comprehensive History overall. You can have all the ROS and Exam elements in the world and still not have the requirements to bill even a 99213, if the HPI/PFSH and MDM aren't equivalent.
The MDM is the most important factor in code selection, so it's really going to tip the scale one way or another, depending on the severity of the condition, how much/what kind of diagnostic work is involved, and the risk of the condition and/or its treatment.
For example, if a patient comes in with the sniffles, and the doctor takes a comprehensive history and performs a comprehensive exam, you're not going to bill a 99215, just because 2/3 key components are documented. The minimal MDM would drag that code down significantly - it wouldn't be medically necessary to bill more than a 99212 or 99213 (depending on the details of the visit and plan of treatment). So, if the doctor overdocuments, then they're wasting their time a little bit, but only because it doesn't change anything in the end. (If they wouldn't send someone to have an unnecessary test run, then they probably shouldn't examine things that aren't relevant, either, but if they want to do it, that's their call. You might talk with them about billing a routine exam, if the patient decides they need a full checkup while they're in there for something trivial, so they could get credit for the extra work.)
Just keep in mind that the ROS and Exam are not everything with code selection, so getting creative with the credit you give on them may not be helpful. The ROS is only 1/3 of what makes up the overall history level (well, 1/4, if you want to get technical and count the chief complaint), and the history and exam together shouldn't determine the level of E/M code you pick, if the MDM isn't there. That's just my thoughts, though...
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