Smoking fish has occurred for millennia to both add flavor to the seafood as well as preserve it. There are two types of smoking -- hot smoking, which simply cooks the cod, and cold smoking, which preserves it. Cold smoking at home is not recommended because the fish is unpasteurized, and can facilitate the growth of harmful bacteria.
Remove all pieces of skin along with any large bones. It is always better to debone the fish before smoking. Make sure that all blood or internal organs are removed from the fish, and rinse it thoroughly under running cold water, using fingers to gently rub the flesh. Always refrigerate the fish before smoking and do not let it sit at room temperature for more than 2 hours before heating. Brine the cod for 30 minutes before smoking if it is 1/2- to 1-inch thick. Add 15 minutes to this time for each additional 1/2-inch of thickness.
Prepare the smoker with the desired wood chips, half of them soaked in water to create a moist smoke. Turn the smoker to 90 degrees Fahrenheit and place the skinless cod on the grill, according to the manufacturer's directions. Cook for 2 to 3 hours, then increase the temperature to 225 F and cook for 45 minutes, or until the internal temperature of 150 F has been maintained for 30 minutes.
Check the internal temperature of the fish before removing it from the heat. This is the only way to tell if the fish is done smoking and safe to consume. Insert a meat thermometer into the thickest part of the cod, in the middle of the fish. Check that the temperature has reached 150 F for every cod piece being smoked, and that this temperature is maintained for at least 30 minutes before removing from the smoker.
Refrigerate the fish as soon as it is removed from the smoker, or serve right away. The fish must be stored at 38 F or colder in a refrigerator. Wrap in a paper towel or cloth instead of plastic wrap, to reduce the chance of mold growth. The smoked fish can also be frozen once it is chilled -- wrap tightly in plastic wrap, press out all the air, and freeze in sealable freezer bags, or vacuum pack for optimal storage. Store for up to 2 weeks in the refrigerator and up to one year in the freezer.