Although "skunking" is considered a flaw in a beer's flavor profile, skunked beer has no ill effect, whatsoever, on the consumer of the beverage. The main chemical, which produces the skunky flavor, 3-Methyl-2-buten-1-thiol, also known as 3-MBT, is considered harmless by both European and U.S. food safety agencies.
The United States Environmental Protection Agency, notes that all food safety agencies, which have 3-MBT on record consider it safe for consumption.
3-MBT is not naturally present in freshly brewed beer. It is produced by the breakdown of components of the hops used to flavor beer. Not all kinds of hops are susceptible to skunking, but those that are gain a sulphurous odor and flavor upon exposure to sunlight. 3-MBT is similar in odor and molecular composition to the main chemical in skunk spray, thus the term "skunking."