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The harmful effects of walnut trees on other plants have been observed for at least two millennia. The ancient civilizations of Greece and Rome used the walnut for its cytotoxic properties as did residents of the American South for easily gathering fish when they threw cut husks into the water with the fish. However, juglone was not isolated until the 1850s. Two men, A. Vogel Jr. and C. Reischauer, were able to isolate the compound from the walnut tree in 1851. The compound was known as nucin at that time. Juglone was then synthesized and characterized for the first time in 1887 by A. Bernthsen and A. Semper.

While at the Virginia Agricultural Experiment Station in 1921, M.T. Cook found that tomato plants in the vicinity of Juglans nigra were negatively effected, most notably by their wilted leaves. Schneiderhan found that Juglans nigra and Juglans cinerea were damaging apple trees in Virginia. The trees that were within an average of 11.9 meters from the walnut trees were found dead. All damaged trees in their vicinity average about 14.3 meters away. In addition, he found that certain local variations of the apple trees tended to be more resistant to the walnuts.

A.B. Massey observed that the walnut trees in alfalfa fields caused the alfalfa to die away in place of grass. After several other experiments, Massey concluded that the toxic compound found in walnut trees was not easily soluble in water, so the compound in the roots and bark must change chemically after it leaves the tree. It was not until 1928 the compound was identified and confirmed to be toxic to other plants by E.F. Davis.

After the scientific news of the harm walnut trees caused certain crops and trees, there was backlash from the scientific community to refute these findings. On one account, A.G. Miller claimed that the trees that Schneiderhan observed to be harming the apple trees in Virginia were not in fact walnut trees.

The use of walnut tree has historically been used within the field of traditional medicine. In America during the early 1900s, doctors prescribed juglone for the treatment of various skin diseases.