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Guatemala's public hospitals are chronically underfunded, under-equipped, and understaffed. Although they will tend to you in an emergency, wherever possible, seek private medical care. Most big cities have at least a couple of private clinics or hospitals; there's usually at least one English-speaker on the staff. Treatment at such clinics can be very expensive, so medical insurance is a necessity.
Malaria is prevalent in areas below 1,500 meters (4,900 feet)—both Antigua and Lake Atitlán are too high to be at risk. Another mosquito-borne disease, dengue, is also a threat, particularly on the Pacific coast. The best way to prevent both is to avoid being bitten: cover up your arms and legs and use ample repellent, preferably one containing DEET. The CDC recommends chloroquine as a preventative antimalarial for adults and infants in Guatemala. To be effective, the weekly doses must start a week before you travel and continue four weeks after your return. There is no preventative medication for dengue.
In Guatemala it's best to drink only bottled water, called agua purificada or agua mineral in Spanish. It is available even at the smallest stores and is much cheaper than in North America.
The major health risk in Guatemala is traveler's diarrhea, so skip uncooked foods and unpasteurized milk and milk products. Ask for your drinks sin hielo, meaning "without ice." In Guatemala most top-of-the-line hotels have ice that's perfectly safe. Pepto-Bismol or Imodium (known generically as loperamide) can be purchased over the counter in Guatemala, but bring along your own stash in case you aren't near a pharmacy. Drink plenty of purified water or tea—chamomile is a good folk remedy. Pharmacies also sell sachets of rehydration salts (suero oral), or you can make your own: ½-teaspoon salt (sal) and 4-tablespoons sugar (azúcar) dissolved in a quart of water.