I understand that the common wisdom nowadays is to cook stuffing separately from the turkey.  Why?

--Karen

In order for salmonella and other bacteria to be killed, most food, including turkey,  should be cooked to an internal temperature of 165°F (74°C).  The temperature should be measured at the center of the food.

The ideal cooking temperatures for turkey are 165°F (74°C) for breast meat and between 175°F (80°C) and 180°F (82°C) for the leg and thigh.  At those temperatures, the light and dark meats are at their most tender and moist.  Above those temperatures, the proteins start to tighten, squeezing out moisture and leaving the meat drier.  At approximately 12 - 15 minutes per pound (27 - 33 minutes per kg), an 18 pound (8 kg) turkey will take between 3 ½ and 4 ½ hours to cook¹.

So, here is the problem.  During the time a stuffed turkey is sitting in the oven, juices from the meat, possibly contaminated with salmonella or other nasties, are soaking into the stuffing.  Since the food is in a nice warm environment, the bacteria will grow even faster than normal.  By the time the breast meat reaches its ideal temperature the stuffing has been acting as a bacteria culture for around three hours or so.  If you go for the higher temperature on the thigh meat, it has been sitting even longer.

Instead of measuring the temperature at the the center of the breast or thigh, you need to measure the temperature in the center of the stuffing.  Because the heat had to penetrate the breast and thigh to get to the stuffing, by the time it is thoroughly heated, the meat is likely overdone.

The other problem with stuffing inside a turkey is that if it is not thoroughly cooked and then is left inside the cavity, it can contaminate the leftover turkey.  Stuffing should always be removed from inside the cavity before the leftovers are refrigerated².

The easiest way to avoid this dilemma is to cook the turkey and the stuffing separately.  Prepare the stuffing as normal but keep it refrigerated in a covered casserole dish until about a half hour before the turkey is finished.  Then put it in the oven and let it cook while the turkey finishes and rests before carving.  All together that should give you about a full hour of cooking.  Check to be sure that the stuffing has reached at least 165°F (74°C), and if necessary cook it a bit longer.  If you miss the taste of the pan juices soaked into the stuffing, you can pour some into the stuffing from the bottom of the roasting pan when the turkey comes out to rest before you make the gravy.  Also, if you want, you can take the lid off of the casserole for the last 20 minutes or so to brown the top.

I make a version of the Mashed Potato Stuffing I had the first time I went to Christmas with my future in-laws.  This year at Thanksgiving there were rave reviews about the stuffing, which had been cooked outside the turkey as described above.

^1. Always use a thermometer to measure doneness.  Cooking times are approximations for planning.

^2. If you absolutely must cook the stuffing inside the bird, you can use a stuffing bag to make removal and serving easier.