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Tokyo is probably one of the safest big cities you will ever visit, and Japan in general is one of the safest places to visit in the world. Most people, including single female travellers, would not encounter any problems walking along the streets alone at night. Street crime is extremely rare, even late at night, and continues to decrease. However, "little crime" does not mean "no crime", and common sense should still be applied as anywhere in the world. Often the biggest risk is travellers taking Japan's visibly apparent lack of crime too close to heart and doing things they would never do back home. The most common crime is sexual harassment on crowded trains. When people are pressed up against each other, hands wander. This is more of a local problem as westerners are considered more aggressive and more likely to stick up for themselves. The best way to deal with any wandering hands is to yell "chikaan" which is a widely publicized Japanese term for sexual harassment, specifically groping on trains.
Small police stations, or Koban, can be found every few blocks. If you get lost or need assistance, by all means go to them; it's their job to help you! They may, however, have difficulties with English, so some knowledge of the Japanese language helps.
Take the usual precautions against pickpockets in crowded areas and trains. Also be aware that theft is more likely to occur in hangouts and bars popular with travellers and non-residents.
The red-light and nightlife districts can be a bit seedy, but are rarely dangerous. Note some small, back-street drinking establishments in red-light districts have been known to charge extortionate prices. Similar problems exist in the seedier upscale clubs in Roppongi, where it may be wise to check cover charges and drink prices in advance.
Don't go into dark areas alone.
If women use common sense they will be safe in Tokyo. Much safer than any US city. Don't walk down dark alleys alone at night, etc. Use a buddy system if you are drinking. If you get "molested" (butt grabbed) on a train make a scene in any language. The grabber will be embarrassed by the attention.
Stay in well populated areas so that you can ask for help or directions if you need it. There is usually always a "Koban" = Police box, on most streets if you have trouble. Most restaurants have fake food displays and picture menus, so it's easy to order. Most attractions have English pamphlets and info, you just have to ask for it. Keep your cards, cash, travelers checks and passport close at hand.
If you worry about losing personal things, put a small label on them identifying them as yours in case it's lost. I lost my wallet twice and got it back both times with all my money and cards. Japan is generally safe. Just use regular caution. I have never experienced sexual harassment. If people, men or women look at you, it's because you're a foreigner and b. they're curious, just looking. Occasionally you will see drunk business men on the train or road, just avoid them. Keep a memo with the name and address of the place you are staying in case you get lost or want to take a cab. Many people speak a little English.
Getting lost in the subway
Getting lost in the sub-way (metro) system as it is very complicated with many lines. Trying to figure out how to get to your destination is a challenge.
Running out of money
Running out of money because the things in Tokyo are expensive. Use your credit card if possible so that you have enough cash just in case.
Language problem as most do not speak English, but the people are very friendly and helpful, and sign language does help. If you want to communicate, use very simple English or just mention the place you want to go e.g. Shinjuku.
Beware of the crowds
Beware of the crowds, especially in subway trains which can be jammed packed and famous places such as Shinjuku, Harajuku which can besuperpacked especially during weekends.
Danger at Tsujiki Fish Market
When you are at the famous Tsujiki Fish Market, do be careful of the moving trucks and other vehicles as this is a very busy fish market. Some of them are moving very fast, so keep an eye while you explore the place.
With your kid
There are a few things to watch out for with your kids.
Folks drive on the “wrong” side of the road for us North Americans. Even older kids used to crossing a street need to slow down and remember to look the, um, “wrong” way first. Many Japanese street are narrow and without sidewalks. Keep a close watch on little ones.
Trains and subways have automatic doors that can whack a small kid, or catch an arm or shoe.
Taxis have back doors that swing open automatically. If your child is too short such that the cabbie can't see her, he might pop that door open and hit her smack in the face curbside (another “safety” tip is to be careful when you use a taxi—the flag drop cost is about US$6 and a ride that sees you stuck in traffic can run up a mighty bill in a hurry).
Many train and subways stations have no escalators or elevators, so be prepared to carry a small child, a baby stroller or a tired spouse. While it is very easy to avoid eating meat while in Japan, it is very, very hard to avoid all seafood. A friend whose child is allergic to peanuts complains that few products have full ingredient descriptions on them, even if you can read Japanese. Be careful with allergies.
Trains, buses and subways can get very crowded. Be careful if your child stands at about the right height to get whacked by a briefcase or shopping bag carried by a fellow passenger. Weekday mornings, from 07:00-09:00 are the most crowded times.