Your teeth can become discolored by stains on the surface or by changes in the tooth material. Extrinsic discoloration — This occurs when the outer layer of the tooth (the enamel) is stained by coffee, wine, cola or other drinks or foods. Smoking also causes extrinsic stains. Nov 10, - Find out why brown spots on teeth happen and what you can do to prevent them. Tobacco is a common cause of surface stains on teeth.