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The short answer from a dietitian
A: Cooking stuffing in a baking dish is the easiest way to make sure it is thoroughly cooked. If you want that special flavor you can only get from putting stuffing in the bird, it is safe to do so if you apply food safety tips.
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If you put stuffing in the turkey, do so just before cooking. Avoid pre-stuffing.
Insert a food thermometer into the center of the stuffing to make sure it reaches 165 degrees Fahrenheit. Bacteria can survive in stuffing that has not reached 165 degrees that could then cause food poisoning.
After removing the bird from the oven, wait for 20 minutes before taking the stuffing out of the turkey’s cavity; it will cook a little more this way.
— Dietitian Maxine Smith, RD, LD
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