Bread
Comehiro – Musashisakai
Hours 9:00~18:30
Melon bread, donuts, loafs, cheesecake, pizza bread.
http://www.comehiro.com/

Cafe
Three – Aoyama
Hours – Breakfast 8:00~11:30
Lunch 11:30~15:00
Dinner 15:00~22:00
They are open all day but have different menus available at different times, but some items that are available all day include:
Pancakes, Chocolate Scones, French Toast all of which are gluten free!
http://aoyama.threecosmetics.com/dining-menu/

Kogomebana – Shirokane-Takanawa
Hours 11:30 ~ 15:00/17:00
Lunch, sweets.
http://kogomebana.com/

Cakes
Otaco Sweets – Tokyo Skytree
Hours 10:30 ~ 18:00
Chiffon cake
http://otaco-sweets.com/

Wara – Kasai & Nakaitabashi
Hours 10:00 ~ 21:00
Sponge cake, flavours such as caramel, sweet potato, kinako, plain.
http://waratokyo.jp/
Please note not all of their products are wheat free, some are a 80:20 mix or rice flour and wheat flour.

Crepes
Gluten Free Cafe Little Bird – Harajuku

Hours 11:00 ~ 22:30
Sweet & Savoury Crepes
https://www.facebook.com/cafe.littlebird/timeline

Pasta
Kakurenbo – Machiya
Hours – Lunch 11:00 ~ 15:00 (Mon-Fri)
11:00 ~ 16:00 (Sat)
– Dinner 18:00 ~ 23:30
Rice pasta and other italian dishes
http://kakurenbo.robust-inc.com/

Pizza
Pizzakaya – Roppongi
Hours – Lunch 11:30-14:00
– Dinner 17:00~23:00 (Mon-Sat)
17:00 ~ 22:00 (Sun)
Gluten free pizza bases and Vegetarian.
http://www.pizzakaya.com/en/

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