The first thing you'll notice about grocery stores (or suupaa, as they’re called) in Japan is that they're a lot smaller than ones in the US. Now that's to be expected in places like Tokyo where there usually just isn't enough room for a giant store. However, even in places that have plenty of space the biggest grocery stores are rarely more than 1/3 - 1/2 the size of your average Safeway, City Market, or any of the other big US grocery store chains. The stores aren't the only thing that's smaller. If you go into any US grocery store I'm sure you're all used to seeing two things by the entrance, those plastic hand baskets you can use to carry around groceries if you don't plan on getting much and the nice big shopping carts. Japan has the plastic baskets (which are pretty much identical) but carts are completely different. A Japanese shopping cart is nothing more than a small metal frame with wheels that you can use to hold one or two of those plastic baskets (since I first came to Japan, some US stores have started using these frames too). So, unless you want to try pushing multiple carts around at once, your entire purchase is limited to what you can fit in one (or maybe two) of those plastic baskets.
Now people in Japan eat more or less the same amount of food as Americans do (mostly different things though), so what’s the reason for the smaller baskets? Well, in Japan people really like fresh ingredients. Part of the reason for this is that many apartments don’t have room for the full size fridges, freezers, and large pantries we have in the US. My first apartment in Japan had a fridge/freezer about the size of the ones you find in hotel rooms and even the larger fridge in my current apartment is still much smaller than any I’ve ever had back in the US.
There’s also some tradition which plays into it. In Japan, the “ideal” family is still one where the husband works and the wife manages the household. When I say manage, I mean a bit more than just cooking, cleaning, and taking care of the kids (though that’s certainly part of it) and there are quite a lot of married working women these days as well, but Japanese family life is a subject best left for another day. Anyway, the point is that when you combine a lack of storage with a stay at home wife and a general love of really fresh food, it makes sense for the wife to go out every day to buy ingredients for just two or three meals at a time.
And, as long as I'm talking about size, it's worth noting that food often comes in smaller packages than in the US. For example, ice cream never comes in anything bigger than a pint and even those are pretty rare, with most ice cream coming in little personal size containers (about the equivalent of a large scoop). And you’ll never find galleon sized containers of juice or milk. About the only things you can find in large quantities are rice and a few other long lasting Japanese staples (such as soy sauce).
Naturally, Japanese grocery stores sell mostly Japanese food (big surprise there). You can find a little bit of American and Italian stuff such as cereal and tomato sauce, but don't expect much of a selection. There are also some Japanese knock offs of said American and Italian items, which are typically cheaper but usually doesn't taste quite the same. Then there are some American staples, such as peanut butter, turkey, pretzels, and root beer, which are almost impossible to find.
Every grocery store also has large selection of cheap boxed meals, or bento, which are very popular both with commuters and some school kids. Bento are made fresh every day at the store and come in all types but a few common kinds include sushi, onigiri (rice balls), and various noodle and rice dishes. They tend to cost only several hundred yen (several dollars) a piece and are usually very good.
Many grocery stores also have their own bakery. Japanese bakeries are a lot different than US ones and I’ll be giving them their own write-up another time so for now suffice it to say that said bakeries include mostly buns, pastries, and snack type breads. Another thing many grocery stores have is little sweet shops that sell small cakes and the like. Once again, most of these items are made fresh daily in the store.
Prices really depend on what you're getting. Some things like seafood, which Japanese grocery stores have an excellent selection of, are very cheap (at least compared to the US) while others are extremely expensive (ice cream and many kinds of fruit, for example). Speaking of fruit, make sure you don't get the regular fruit mixed up with the gift fruit. Gift fruit is typically very big, very nice looking, and very very expensive. As the name suggests, you get it to give as a gift, not to eat yourself, and it’s typically sold in packs of one or two. Speaking of prices, it’s worth noting that, because of the love of fresh food, Japanese grocery stores often offer heavy discounts on many unsold products such as bento and meat shortly before closing time.
When you're ready to pay for your groceries you go to the cashier, takes your plastic basket off your cart, and stick it on the counter. The cashier then scans your items (reciting the price of each one as he/she does) while putting them in a new plastic basket. Then they'll often stick some plastic bags into your new basket (the magic number of bags seems to be two, at least that's the amount of bags I get 95% of the time regardless of how much I buy). If it looks like you're getting something that you might be eating soon (say a bento box or an ice cream cup) they'll add in a free set of chopsticks or a spoon as well.
After paying, you take your basket to a nearby bagging area, which is basically a counter or table where you can put your basket while you transfer the contents from it to your bags (if the cashier didn’t give you any bags, they’ll be waiting for you here). Said tables usually have a damp cloth you can use to wet your fingers if you're having trouble getting a bag open and a place to put your basket once it's empty. After that, you're ready to grab your bags and head out (if you had a cart, remember to wheel it back to its place by the entrance).
And that's how you buy groceries in Japan. Personally, I love the bento, bakeries (which make far better bread than you’ll find in Safeway or City Market), and large selection of Asian foods. I’m less thrilled about the tiny package sizes, lack of peanut butter and a few other things I really love, and the extremely limited selection of things like cereal and cheese. So there’s certainly good and bad points. But if you’re ever in Japan, even if you plan on eating out for most of your meals, it’s worth it to take a look in a Japanese grocery store just to see all the new and different kinds of food.