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Japan is a safe, clean country for travelers with good drinking water and no major water- or insect-borne diseases. Drugs and medications are widely available at drugstores, although the brand names and use instructions will be in Japanese, so if on regular medication, take along enough supplies to cover the trip. As with any international travel, be sure to bring your prescription or a doctor's note just in case. Condoms are sold widely, but they may not have the brands you're used to. Speak with your physician and/or check the CDC or World Health Organization Web sites for health alerts, particularly if you're pregnant or traveling with children or have a chronic illness.
Specific Issues in Japan
Japan is basically a safe country for travelers. The greatest danger is the possibility of being caught up in an earthquake and its resulting tsunami. Earthquake information is broadcast (in Japanese) as news flashes on television within minutes, and during major disasters national broadcaster N.H.K. broadcasts information in English on radio and television. Minor tremors occur every month, and sometimes train services are temporarily halted. Check emergency routes at hotels and higher ground if staying near coastal areas.
Tap water is safe everywhere in Japan. Medical treatment varies from highly skilled and professional at major hospitals to somewhat less advanced in small neighborhood clinics. At larger hospitals you have a good chance of encountering English-speaking doctors who have been partly educated in the West.
Mosquitoes can be a minor irritation during the rainy season, though you are never at risk of contracting anything serious like malaria. If you're staying in a ryokan or any place without air-conditioning, anti-mosquito coils or an electric-powered spray will be provided. Dehydration and heatstroke could be concerns if you spend a long time outside during the summer months, but isotonic sports drinks are readily available from the nation's ubiquitous vending machines.
It may be difficult to buy the standard over-the-counter remedies you're used to, so it's best to bring with you any medications (in their proper packaging) you may need. Medication can only be bought at pharmacies in Japan, but every neighborhood seems to have at least one. Ask for the yakyoku. Pharmacists in Japan are usually able to manage at least a few words of English, and certainly are able to read some, so have a pen and some paper ready, just in case. In Japanese, aspirin is asupirin and Tylenol is Tairenoru. Following national regulations, Japanese drugs contain less potent ingredients than foreign brands, so the effects can be disappointing; check advised dosages carefully.
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