Artificial flavors are typically not harmful. However, I'm not crazy about them, because they don't usually reproduce the natural taste of foods and are often markers for low-quality foods. Whether natural or artificial, food flavors are made up of molecules that occur naturally and can be synthesized. In general, natural flavors are much more complex than artificial ones, which have far fewer component molecules.
Artificial flavors may be more stable than natural ones and certainly are less expensive, so manufacturers prefer them, and many consumers are satisfied with them. There is even a weak case to be made that artificial flavors are safer for consumption because they omit components of natural flavors that may be slightly toxic.
If a food product contains artificial flavors, you should check to make sure that it doesn't also contain less desirable additives. Read labels carefully to check for high fructose corn syrup (HFCS) used to sweeten soft drinks and juices. HFCS contributes to obesity in many people.
Also, watch out for artificial colorings and dyes (look for the terms "artificial color added," "U.S. certified color added," "FD & C red no. 3" (or "green" or "blue" or "yellow" followed by any number), as well as artificial sweeteners and monosodium glutamate (MSG). I'm suspicious of chemicals used to dye foods. They are a group of highly reactive molecules that may interact with DNA and increase mutation or cell transformation. Read labels and avoid them.
Andrew Weil, M.D.