Just over two years ago we came across a great place to stay in Kyoto.  Di found it by accident as the name of the place does not ring Japanese.

Its a small guest house in North Kyoto called Casa de Natu.  It was originally the owners parents house and she has been lovingly restoring it over the years.  It a very traditional old house, and has two main bedrooms downstairs.  There are two rooms upstairs, but she tends not to let them out as they don’t have direct access to the bathroom (except via the other two bedrooms). 

The price is very reasonable 4500yen per person per night and includes a simple breakfast.  The location is north of the city centre, but is located well to subway and bus.  The neighbourhood is very nice and quiet with a good select of restuarants and coffee shops.  If you are looking for a place thats away from the crowds of Kyoto (and lets face it when is Kyoto not filled with tourists) this is an ideal location.  We have found on the occasions we have stayed there thats its very easy to get to the locations you want to and with some careful use of the subways and buses you can avoid alot of the crowds (or surf ahead of the crowds as we call it).  

The owner is wonderful and speaks English well. She has a basic website (link above) and will accept bookings via email.  The directions are a little tricky the first time getting there, but she will send you a map.  Its a really great way to stay in Kyoto in a traditional old house.  The accomodation is simple and comfortable and even now its getting cold there you have a snug nights sleep!