I've been getting a few emails from people wanting tips about fabric shopping in Tokyo, so before I forget my way around the city I thought I'd do a post with as much information as I can remember in one place.
I did most of my fabric shopping at two places, Marunan in Shibuya and Yuzawaya in Kichijoji. I lived in Ebisu, so these were both really handy for me. Marunan is at Shibuya crossing, so it's easy to get to no matter where you're staying in Tokyo. Take the Hachiko exit from the JR station, and then you get to a huge pedestrian crossing with a big Starbucks opposite. Cross over the road to the left, towards the 109 building, and you'll see Marunan on the left, with some rolls of fabric outside. There are about 5 floors, with notions and ribbons at the top, and printed cottons for patchwork in the basement. It is not incredibly cheap, but much cheaper than Japanese fabrics are overseas. This shop is really good if you have limited time in Tokyo and want to buy fabric without going too far out of your way.
Yuzawaya is a chain of big craft stores, and the Kichijoji branch is the only one I ever visited, although I know there are lots of others. The easiest way to get there is to catch the Inokashira line from Shibuya - the line goes from Shibuya to Kichijoji so it doesn't matter which train you get, although the express is quickest. It usually takes about 20 minutes to get there. When you get off the platform, go through the ticket barriers and head up a flight of stairs to your right, past a Starbucks, and you end up in Yuzawaya which is actually in the station complex. You will enter on a floor that is mostly thermal underwear, but do not be peturbed - crafty goodness is just upstairs! There are floors and floors of fabrics, wool, beading, kits and all kinds of things, and then stationery in the basement. It is possible to spend all day here, as well as lots of money. If you want to venture out and explore Kichijoji it is a great area - Kat has some excellent links to other local crafty stores and businesses (scroll down to "Let's go Kichijoji"). And if you are overwhelmed by fabric shopping you can go rent a swan boat and chill out in Inokashira Park.
The other big area for fabric shopping is Nippori, which is in northern Tokyo up near Ueno. Catch the JR Yamanote line to Nippori and then follow the signs to "Nippori Textile Town". If you end up in a big graveyard you've come out the wrong side of the station, but not all is lost because you are on your way to Yanaka which is my very favourite area of Tokyo and well worth an excursion anyway. If you want to go to Yanaka you can visit here and here and have coffee here as well as pottering around the old wooden houses, shops and shrines, but for fabrics you should head back to the Textile Town, which is a street full of smallish fabric stores except for the huge and impressive Tomato. It has a fantastic range of fabrics, especially cute cotton jersey, printed cottons and oilcloths. Be warned - bring cash! They don't take cards.
Vintage kimono and obi can be bought cheaply at most fleamarkets, especially if you are buying them to chop up and don't mind a bit of damage. I found them at the Togo Shrine market in Harajuku and the Hanazono market in Shinjuku, but they seem to be a fixture at all markets. There is more information on Tokyo fleamarkets here and here.
So, those are my tips for fabric shopping in Tokyo, but they are very much based on my own experiences, and since my Japanese is not so good I mostly relied on word-of-mouth recommendations and places I stumbled on. If I've got anything wrong (directions are not my strong point) or you have other suggestions please leave links and comments below!
Update: for knitters, Kat has a great list of yarn stores.