Many group practice organizations use physician protocols to standardize medical practice within the group. The goal may be to improve consistency of care when a patient is likely to be seen by different doctors, to limit the number of drugs in the formulary, or to ensure that the physicians are following recognized standards, such as Centers for Disease Control (CDC) protocols, in their practices. Physician protocols do not place legal limitations on the physicians; they are characterized by their allowance for independent medical judgment. They are a voluntary or contractual agreement by the physicians to follow certain patterns when practicing within the group.

A common example is a protocol for treating an MCO patient for essential hypertension. Typically this protocol would not include a definition of essential hypertension; every treating physician would be expected to be able to make the diagnosis. The protocol would contain a list of the diagnostic procedures to be done on a new patient. These might be arrived at by consensus after an analysis of the costs and benefits of each test. Every patient might have a blood count but only those over age 40 years would have an electrocardiogram. The protocol would then list the drugs to be prescribed for certain types of patients. A beta- blocker might be first choice, with an alpha- blocker substituted if the patient does not respond well or is over 60 years old. The drugs on the list also would be in the formulary.

The physician protocol guides rather than dictates patient care. If a physician wants to use a different drug from the established standard, the reasons for deviation should be documented, but the physician is legally free to make the change (subject, however, to discipline by the MCO). In contrast, an NPP would not be allowed to use such a protocol becasue it leaves the diagnosis open and allows choice in the use of medicines, both of which require exercising medical judgment.