Since the meridians run along certain routes and pertain to certain viscera, there is a special relationship between different parts of the body and the internal organs. Clinically the relationship between the pathological location or the disease and the meridians can be used to decide which meridian and viscus are involved so as to make an accurate diagnosis. For example, the liver meridian distributes over the hypochondrium, so hypochondriac pain indicates liver disease; the lung meridian emerges from the supraclavicular fossa, pain in the supraclavicular fossa indicates lung disease. 

Take headache for another example. It usually appears in different regions. Pain in the forehead is related to the yangming meridian; pain in both sides of the head is usually related to the shaoyang meridian and pain in the nape is often related to the taiyang meridian. Besides, some diseases show special reaction points on certain acupoints. If tenderness appears on these reaction points, it is very helpful for diagnosis. For example, intestinal abscess will lead to tenderness on Lanwei (EX-LE7), gallbladder disease will bring on tenderness on Yanglingquan (GB 34).

The theory of the meridians and collaterals is extensively used in clinical treatment, especially in acupuncture and moxibustion, massage and drug treatment.

The treatment of disease by acupuncture, moxibustion and massage is usually done by needling or massaging the acu-points proximal or distal to the affected part on the meridians to regulate the functional activities of the meridian qi and blood. To select acu-points, one has to differentiate the syndrome first with the theory of the meridians and collaterals to decide which meridian the disease is related to, and then select acu-points in the light of the running route and coverage of the meridian. Such a way to select acu-points is called "selection of acu-points along the meridians".

Drug treatment also has to be done according to the theory of meridians and collaterals because the meridians and collaterals can transport the effect of the drugs to the affected part. In the long course of clinical practice, TCM has developed the theory of "meridian tropism of drugs" which holds that each drug can enter one or more meridians. With the guidance of this theory, clinically drugs are selected, based on syndrome differentiation, according to their state of "meridian tropism" to treat disease so as to improve the therapeutic effect. Again take headache for example. 

If it is related to the taiyang meridian, Qianghuo (Rhizoma seu Radix Notopterygii) should be used; if it is related to the yangming meridian, Baizhi (Radix Angelicae Dahuricae) should be used; if it is related to the shaoyang meridian, Chaihu (Radix Bupleuri) should be used, because these drugs enter to these meridians respectively. In the formulation of a prescription, one or two drugs that enter a certain meridian can be added in order to guide the other drugs, which normally do not enter that meridian, to work on that meridian. The drug that leads other drugs to work on a certain meridian or organ is called "guiding drug".