If you or someone you are travelling with has coeliacs disease (gluten intolerance), then Japan will seem a daunting prospect.  Because coeliacs is largely limited to Western countries, much of Japanese cuisine is off limits, because tempura, tonkatsu and all of those tasty bakery treats have wheat/flour in them.  Adding to the difficulty is that the Japanese generally know nothing of coeliacs disease.  The good news is that gluten-free travel in Japan can be done.

A caveat for the following: Coeliacs will quickly point out that to be truly gluten-free requires avoiding soy sauce, unless guaranteed it doesn't contain gluten.  Whilst that is true, experience suggests small amounts of soy sauce containing gluten cause limited problems and the reality is that unless you want to spend more time searching for food than enjoying the wonders of this country - a few risks have to be taken.  Some people use cards that have an explanation of coeliacs written in Japanese and then hand the card to the waiter/chef and hope they will cater for your needs.

Breakfast

Given this meal is likely to be the most problematic - it gets its own section.  Most hotels will offer contintenal breakfasts, but obviously most of the items provided will not be suitable.  Those incredible looking bakery items that are everywhere in Japan are obviously not going to work.  There are really three options:

The first is sushi and other rice-based snacks that are easily found in convenience stores and major train stations. There are triangle shaped large sushi items that work well, but some are completely covered in rice/sea-weed, meaning you can't see what the filling is (often it's only pickled vegetables or smoked salmon). Train stations like Ueno have all kinds of sushi on offer and if you don't want to start the day with sashimi, then try sushi full of pickled vegetables or the delicious inari (there's a shop at Ueno Station that just sells inari, which is flavoured rice wrapped in sweetened fried tofu).

The second option is to buy cooked vegetables or salad from the wonderful food floors in the major departments stores (for instance, around Shibuya) or in major train stations (Ueno again is a winner). The good part about this option is you can see the food before you buy it and gauge what is in it.  The bad news is that this isn't the cheapest or most filling breakfast.  

The final breakfast option is to get accommodation where you can cook your own breakfast.  This is surprisingly affordable in Kyoto and Osaka, where there are cheap and decent serviced apartments that have a small kitchen in your room (hot plate, microwave, fridge, crockery, utensils and pans). See for instance Citadines in Kyoto and the Fraser Residence in Osaka.  A visit to the local supermarket will provide the ingredients you need to make your own healthy breakfast, or try bringing a GF pancake mix from home.

Tokyo

In a city of between 14-30 million people (depending on what you count as Tokyo), it is no surprise that with a little searching, you can find anything and everything to eat.  Alas, the one thing you may not come across is a gluten free menu in a restaurant or a GF section in a supermarket.  The solution is to eat the non-Japanese foods you know from home are generally safe - Indian, Thai, Vietnamese, Spanish etc.  In terms of Japanese, the only really safe option is sushi and the easiest and least intimidating way to do that is a conveyerbelt style restaurant where you can see what you're about to eat before selecting it (try Heiroku Sushi near Omotesando and Harajuku stations for tasty sushi with English menus and bilingual chefs).  Beyond sushi, some shokudos will have set meals that provide a few things that appear GF (can be risky) and some soba noodles are not only gluten free, but might even have been made without contamination (very hard to tell though).  Luckily, Indian, Thai and Spanish restaurants abound in Tokyo and a useful website for finding them is www.bento.com (English).  For Spanish, there are a chain of Vinuls restaurants, which serve relatively cheap tapas and paella that is seemed to be gluten free (try the great atmosphere of their restaurant under the station at Ueno).  

Kyoto

Unfortunately Kyoto's plethora of wonderful temples is not matched by an equal number of gluten free options. The best options are found around the shopping malls of downtown.  Check out the tripadvisor and/or bento.com listings for the following: Kerala (Indian), Yak and Yeti (Nepalese) and Kati (Thai).  For easy to order sushi that is cheap at lunch, try Musashi.  Whilst Kyoto isn't the easiest for coealics in terms of food, it is fanastic for drinks.  For really decent coffee in a nice atmosphere, google Cafe Bibliotech Hello.  Just around the corner is a simply brilliant spot to try the gluten free Japanese drink that is sake - Yoramu, which is run by an Israeli expat who provides a wonderful introduction to the complexities of sake.  

Osaka

Osaka's food and drink options abound.  Google Krungtep (or Krung Tep) for an extensive thai menu in Osaka.  If you're staying near Namba station, in the ground floor of The Fraser Residence hotel is a well priced tapas place with an English menu and a number of tasty paellas (this place is a chain, but the name escapes the author).  There are a wealth of dining options, including conveyerbelt sushi on the food levels of the Namba Parks shopping centre and the smaller place that is next door.

Outside of Major Cities

Eating gluten free becomes much harder outside the larger cities.  Beyond Tokyo, Kyoto and Osaka, in places like the Hakone region around Mt Fuji and Hiroshima. Even if only for a day trip, Hakone is really difficult, as there are very few non-Japanese options and lots of tempura!   If based in Kyoto, Osaka or Tokyo, there are many good day trips to be done.  A tip - buy sushi, a bento box or salad/vegetables from a supermarket or department store dining food floor before you catch your train.