In general, occasionally writing on skin with water-based inks is considered non-hazardous. Concern arises when people writewritewrite 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 aaa 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 aaa 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.
http://www.wisegeek.com/is-it-true-that-writing-on-skin-is-unhealthy-or-risky.htm