Shops during Christmas and New Years

I will be visiting Japan during Christmas and new years and wondering if the shops will be open?

Everything is open over Christmas. Many shops are closed on January 1, but not all. Some smaller shops may close multiple days over New Year, but most re-open on the 2nd. It is also explained here:
http://www.japan-guide.com/e/e2276.html

Be aware of your destination on New Year. Many shops and restaurants close for one of more days.

Be wise to ask your hotel/inn if specific restaurants open during the holiday season. Or else you might have to rely on restaurants along main drag or combini for meals.