AK is generally believed to be free of direct adverse effects, although the potential exists for it to be harmful indirectly by delaying the appropriate diagnosis of serious conditions.

AK should not be relied upon as the sole diagnostic or therapeutic approach to potentially serious conditions instead of more proven methods, and it should not delay the time it takes to speak with a qualified healthcare provider about such conditions.

Applied kinesiologists theorize that physical, chemical, and mental imbalances are associated with secondary muscle dysfunction - specifically a muscle inhibition. Muscle inhibition is when a muscle is blocked or suppressed.

AK practitioners may evaluate the health status of patients according to three health factors: chemical, mental, and structural. It is proposed that ill health may result from an imbalance in these factors. Joint manipulation or mobilization, myofascial therapies, cranial techniques, meridian therapy, clinical nutrition, dietary management, or reflex procedures may follow the practice of AK. Environmental or food sensitivities may be evaluated by muscle testing.

Although scientific study of applied kinesiology is limited, there is a growing body of research to suggest that applied kinesiology is not effective for the diagnosis of medical conditions. Some research suggests that it may not be possible to diagnose underlying diseases based on muscle responses. Other reports note that the diagnoses made by AK practitioners are not consistent, and do not accurately reflect the nutritional status of patients. Because nearly all AK tests are subjective, many regard the practice with skepticism.

Body talking tests muscles as a diagnostic method. Commonly, patients lie down and raise their dominant arm.

The arm-pull-down test is considered by the International College of Applied Kinesiology (ICAK) to be a very poor form of muscle testing. The arm-pull-down test involves many different muscles making it difficult to distinguish the muscle with the problem. Through evaluation of the function of specific muscles pre- and post-treatment throughout a patient's body, therapeutic effectiveness for particular problems may be assessed.

Applying the proper therapy results in improvement in the inhibited muscle. Scientific, repeatable and accurate muscle testing requires the specific isolation of a muscle before it is tested. Next, the AK practitioner instructs the patient to resist as the tester places downward force on the subject's arm. The tester subjectively evaluates the force exerted by the subject to determine the strength of the muscle. This is supposed to give a baseline for further testing.

The AK practitioner performing the test applies pressure opposite the patient, but this practitioner is also the one who decides whether one push is stronger than another.

Much of the subjectivity in manual medicine has been overcome by the use of manual muscle testing as a diagnostic indicator.