Shoki has always been a favorite of mine. They recently updated their menu to include miso in some of their ramen broths and it's GREAT. The GF selection and options have greatly expanded, they now make their own GF rice noodles. Definitely Celiac friendly and they take the mention of allergy seriously. The menu is clearly labeled and the staff are knowledgeable.
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I think they have two gluten free items, but you'll want to double check that. Anyway I always get the gluten free tan tan men and its amazing! They offer yam noodles in place of regular noodles (as well as white or brown rice). None of the meat is gluten free, but they do have tofu (as well as other toppings that are safe to eat). They're also very good at dealing with food allergies and have a very knowledgeable staff. I absolutely love it here!
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