This allows the submucosal tissue plane to be identified after the polyp is removed, which is useful in determining if more tissue needs to be removed, or if there has been a high risk for perforation. Methylene blue is used in endoscopic polypectomy as an adjunct to saline or epinephrine, and is used for injection into the submucosa around the polyp to be removed. At high doses, however, methylene blue actually induces methemoglobinemia, reversing this pathway. Methylene blue can reduce the half life of methemoglobin from hours to minutes. Methylene blue, when injected intravenously as an antidote, is itself first reduced to leucomethylene blue, which then reduces the heme group from methemoglobin to hemoglobin. When large amounts of methemoglobin occur secondary to toxins, methemoglobin reductases are overwhelmed. Normally, through the NADH or NADPH dependent methemoglobin reductase enzymes, methemoglobin is reduced back to hemoglobin.

Methylene blue is employed as a medication for the treatment of methemoglobinemia, which can arise from ingestion of certain pharmaceuticals, toxins, or broad beans. It is on the World Health Organization's List of Essential Medicines. Methylene blue was first prepared in 1876, by Heinrich Caro. While use during pregnancy may harm the baby, not using it in methemoglobinemia is likely more dangerous. Use often turns the urine, sweat, and stool blue to green in color. Other side effects include serotonin syndrome, red blood cell breakdown, and allergic reactions. Common side effects include headache, vomiting, confusion, shortness of breath, and high blood pressure. Methylene blue is typically given by injection into a vein. It has previously been used for treating cyanide poisoning and urinary tract infections, but this use is no longer recommended. Specifically, it is used to treat methemoglobin levels that are greater than 30% or in which there are symptoms despite oxygen therapy.

As a medication, it is mainly used to treat methemoglobinemia by converting/chemically reducing the ferric iron in hemoglobin to ferrous iron. Methylthioninium chloride, commonly called methylene blue, is a salt used as a dye and as a medication.

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