Regarding pertinent negatives:
Both pertinent positives and negatives should be included in the following ares of the patient note: (1) History, (2) Physical Examination, (3) The differential diagnosis (supporting evidence).
The history and physical exam is self-explanatory, the DDx may be more difficult to understand. Take bilateral joint pain of the MCP joints:
DDx 1: Osteoarthritis, pertinent positive - worsening pain with use, insidious onset; Pertinent negative - no constitutional symptoms, no swelling/warmness (also can be used on PE as pertinent negative when you palpate if not present-a pertinent negative).
DDx 2: Rheumatoid arthritis, pertinent positives- bilateral joint involvement, mother with SLE (or any rheumatological disease);; Pertinent negative - no involvement of DIPs (here, since osteoarthritis is high on differential, forget the order for now, relative to OA, this pertinent negative may make RA more likely ( in some cases, pertinent negatives may help a diagnosis be ruled in not by its relative nature to another differential but intrinsic to the disease itself, e.g. step throat, pertinent negative - no cough (which is actually one of the diagnostic criteria for strep... if esophagitis was the other on the differential, no cough is not justifying step throat relative to esophagitis (because cough is often absent from this diagnosis/does not lend much support even if present)-- thus, the absence of cough (a pertinent negative) instrinsically justifies strep throT (so 2 reasons for justifying a diagnosis based on a pertinent negative finding - as in the case above with OA, no fever justifies it RELATIVE to RA, of course assuming that is on the differential.....and in the case of strep, no cough supports this diagnosis intrinsically).
One last comment - I would think that more pertinent positives would be listed vs negatives--but keeping in mind an opportunity to list a negative will certainly make your diagnosis more likely. Some believe pertinent negatives are used to RULE OUT a diagnosis (e.g no tachycardia for PE, say after listing a bunch of positives) -- I do not believe this to be what they are asking.
Please refer to the USMLE website, which put out a pdf on the clarification of this point. These are my opinions and are not fact, refer to USMLE for definitive answers.