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G6PD is a genetically inherited condition, where the body lacks an enzyme and, as a result, SPECIFIC foods and medication can cause the breakdown of the red blood cells in the body if consumed. I do not think that topical application of a dye on the skin will cause the same reaction as taking the specific foods and medication. Please check with your family doctor about the types of food and oral medication that your child needs to avoid. If you were to apply henna, do not use needles and start only with small area. See a doctor if your child experiences any adverse reaction to the henna dye.
The main food to avoid in G6PD deficiency is fava beans, also known as broad beans. Pay attention to foods that are also made using fava beans (it is advisable to check the food labels for the ingredients). Another food that is best avoided is the bitter melon or bitter gourd.