[talz13]

I went last summer, and walking around Shinjuku (a ward of Tokyo) at midnight-1a.m. I felt safer than I do walking around in the middle of the day in the small town that I'm from.

Really, if you just stay to main streets and well-lit areas, you should be fine. I would recommend trying to figure out how the trains and everything work before you go / as soon as you get there so you don't get yourself stranded. I had to talk to the station master a couple times to find out how to get where I was going, but I did KNOW where I was trying to go. And I don't really speak a word of Japanese. I suppose if you need to, keep some papers in your bag with the names of the places that you are visiting (print off the directions to your ho(s)tel, etc.) and then at least you can point to where you're trying to get to and the station master will be able to help you out.