Phenylalanine is the name of one of the 9 essential amino acids. It is found in proteins throughout the body and in most foods that contain protein such as meats, fish, and poultry, milk products, eggs and soy. It is also in some nuts and seeds. Since whey protein is derived from milk, it makes sense that phenylalanine is a component of whey protein powders. Whey is the liquid left after milk has been coagulated to curds and the curds have been removed. Cottage cheese is an example of curds and whey (that's what Little Miss Muffet was eating when she sat on her tuffet).
Due to a rare genetic disorder called phenylketonuria (PKU), manufacturers are required to let consumers know if their products contain phenylalanine. People with PKU are missing an enzyme that is needed to properly metabolize phenylalanine, therefore they must restrict their intake so that phenylalanine does not build up in the body.
Nature provides phenylalanine in combination with other essential amino acids in foods that contain protein. It does not occur in nature as an isolated amino acid. An example of chemically isolated phenylalanine is Aspartame, the artificial sweetener known as Equal and Nutrasweet. Although aspartame does not contain phenylalanine per se, it breaks down into phenylalanine when it is ingested and metabolized. Too much isolated phenylalanine in the body can cause overexcitement of neruons in the brain to the point of cellular death. Research has shown that too much isolated phenylalanine in the daily diet can trigger Attention Deficit Disorder, Hyperactive Disorder, emotional and behavioral disoders.
As for phenylalanine in whey protein powders, the green light is on. Just be sure that you are not a victim of irony by consuming a protein powder that is sweetened with aspartame!