The answer is Yes and No.
Some markers can cause harm. They usually have a very strong chemical smell when you remove the cap.
The Sharpie brand seems to work OK.
I would suggest using the "Ultra Fine Point" as it puts less ink on the disk.
Sharpie brand is available at office supply stores.
I burn audio and data CD-Rs and hand-write labels for them using permanent markers. Does anyone know if, once dry, there is anything in the marker ink that might damage CD-R discs if they are stored simply by being stacked one atop the other, without individual cases? THX JLJ