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Use purified water for drinking and brushing your teeth. If you're out trekking, bring an extra bottle with you. Also, eat foods that have been thoroughly cooked or boiled. If vegetables or fruit are raw, be sure they're peeled. In the highlands, especially Huaraz, relax and take the time to acclimatize for a few days, drinking lots of water to avoid dehydration and altitude sickness.
In the big cities on the coast, be on your guard and take simple precautions, such as asking the concierge at the hotel to get you a taxi and carrying only the cash you need. In small coastal towns or in the highlands things are more secure, but be aware of your belongings at all times.