Japanese manners are many and various, nevertheless, one of the first things you need to know (in order to know what to do) is that: when you go to a japanese house, you must remove your shoes before entering.
This also applies to some restaurants or public buildings, such as medical centers or language centers, as we learnt one day when we had the chance to go to a portuguese lesson and had to remove our shoes in the classroom!
It is a matter of cleanliness, but it is actually very comfortable. Now we know why in Japan there are socks for sale everywhere!
Most japanese houses have in their entrance hall a rack for guests` shoes and some slippers for them. So you will need to remove your shoes there and put on some slippers to walk around the house. (Tip: wear always clean and without-hole socks).
Another very important thing is that there are special slippers for the bathroom. You should leave the regular slippers outside and put on the toilet slippers to enter. Then, don`t forget to change again, or else you will be walking around the house with the wrong ones!