Cockroaches.....need I say more.  They are fast, ugly, and hated World-wide.  But unfortunately, they are a part of traveling and living in Japan.  If you never see a cockroach on your travels, you are very lucky.  However, do not assume they are not there.  All Japanese homes, businesses, hotels, etc, have cockroaches.  Often you will hear them more than see them, as they prefer to avoid the light.  And much to my surprise, they can fly as well.  Ugh!  Yet, no matter how old or new of a building you stay in, where there is food, those pesky critters will be there.  The best way to keep Cockroaches out of your room is to NOT EAT in your room.  Do not order room service at the hotels, and do not keep any perishable foods in your room at  hostel or Bed and Breakfast locations.  You can be in a dark and dust ridden youth hostel but if there is no food lying around and the kitchen is clean, it will be relatively cockroach free.  

In short, if you don't eat in your room, you'll save yourself from meeting these nighttime visitors.   Happy Travels....