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I did some pruning of a couple of thujas for the first time in my life, and I noticed that the chopped thuja leaves have a strong scent that is different than the scent of leaves of other conifers. The scent remained to some extent even after washing my hands. Is that fragrant substance harmful to human skin?

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Maybe, maybe not - some people may experience contact allergy symptoms on the skin from any coniferous plant, including Thuja. Thuja contains oil which has volatile constituents, and its resinous nature means it can be quite difficult to wash it off thoroughly. (In my experience, anything resinous on the skin is better washed off using washing up liquid, a soft nail brush and hot water, rather than just ordinary toilet soap on its own.) It is, though, sometimes used in herbal medicines, though great caution is recommended with its use, since it's essentially toxic. Thuja herb uses and health benefits.

A laboratory analysis of the volatile components can be found here.

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