In general, occasionally writing on skin with water-based inks is considered non-hazardous. Concern arises when people write on their skin frequently with permanent ink, or with inks that have certain coloring agents. If one is writing on skin on purpose, then using skin paint or skin ink is a far better choice, although even water-based inks may cause some skin irritation for some people.
The primary concern with writing on skin with permanent ink is that permanent ink may contain xylene. Xylene is a toxic substance, though toxicity is normally linked to inhalation. A mark or two of permanent ink on the skin because one is using a permanent pen is not likely to cause significant harm.
People can cause damage to their skin however, by cutting the skin and then writing on skin with a permanent marker. This is a type of amateur tattooing that can be very difficult to get rid of and may cause skin irritation and infection. Usually, if this occurs, one must see a doctor in order to get rid of the marking and treat infections.
Some permanent inks now use an alcohol-based substance instead of xylene. While this is less hazardous than xylene, it still may irritate the nose, throat, mouth and sensitive skin. Both types of permanent ink pens are more hazardous if the ink is ingested or large quantities of ink are inhaled. However, most doctors recommend avoiding writing on skin with any type of permanent ink.
Further if one has a child writing on skin with permanent ink, it is very important to ignore most Internet advice given for removing such writing. It will fade in time, or many use alcohol handwash to diminish appearance. Many people suggest using bleach, but this is a very unsafe practice that can further damage skin, and can also be dangerous in small amounts if inhaled.
If a child seems to be unable to avoid writing on skin, keep only water-based, non-toxic markers on hand. Conversely, let the child write on his or her skin with specially designed non-toxic body paint or inks. Water-based inks tend to be easily removed as well.
Scented inks, popular with children, are not a good choice. These, too, can be permanent and may contain xylene or other solvents. As well they may encourage young children to eat their art or suck on the markers. Ingestion of xylene is hazardous.
Dyes in inks can also be a potential irritant. Some inks will now only work on special paper and these are probably the best for children who want to write on themselves or the walls, for instance. With regular inks, such as those used in ballpoint pens, writing on skin is not considered dangerous, though the occasional person might be irritated by the dyes in inks. Normally for such ink to be considered poisonous, one would have to ingest three or four penfuls of ink. The occasional writing on skin with a ballpoint pen, uses a tiny amount of ink, and is thus not considered harmful.