Although doctors have varying approaches as to the sequence of body parts, a systematic examination generally starts at the head and finishes at the extremities. After the main organ systems have been investigated by inspection, palpation, percussion and auscultation, specific tests may follow (such as a neurological investigation, orthopedic examination) or specific tests when a particular disease is suspected (e.g. eliciting Trousseau's sign in hypocalcemia).

With the clues obtained during the history and physical examination the doctor can now formulate a differential diagnosis, a list of potential causes of the symptoms. Specific diagnostic tests (or occasionally empirical therapy) generally confirm the cause, or shed light on other, previously overlooked, causes.

Whilst the format of examination as listed below is largely as taught and expected of medical students, a specialist will focus on their particular field and the nature of the problem described by the patient. Hence a cardiologist will not in routine practice undertake neurological parts of the examination other than noting that the patient is able to use all four limbs on entering the consultation room and during the consultation become aware of there hearing, eyesight and speech. Likewise an Orthopaedic surgeon will examine the affected joint, but may only briefly check the heart sounds and chest to ensure that there is not likely to be any contraindication to surgery raised by the anaesthetist.

A complete physical examination includes evaluation of general patient appearance and specific organ systems. It is recorded in the medical record in a standard layout which facilitates others later reading the notes. In practice the Vital signs of Temperature examination, Pulse and Blood pressure are usually measured first.