Among the best places to visit Peru's share of the Amazon is Manu, a UNESCO World Biosphere Reserve of nearly five million acres. Containing the greatest bird, mammal, and plant diversity of any park on the planet, Manu teems with life (giant river otters, parrots, and monkeys, for starters). The easiest way to visit the park is on a group tour. Tropical Nature Travel is one eco-conscious operator (877-827-8350; www.tropicalnaturetravel.com). Another stunning swath of Amazonian rain forest is the Tambopata National Reserve, where Rainforest Expeditions operates three of the best lodges (877-870-0578; www.perunature.com). While the outfits are admittedly spare to Spartan, they place you—and a crack team of biologist guides—in the middle of some of the most surreal wildlife displays in existence, not least the sunrise macaw-fest at the massive clay lick next to the Tambopata Research Center.

At twice the depth of the Grand Canyon, Colca is the world's second-deepest canyon and home to the world's largest birds, the giant Andean condors, with wingspans of up to 11 feet. Too large to take flight from the ground, the condors become airborne by leaping from cliff perches, which they do each morning between about 9 and 10 am; they then swoop and soar before gliding above the river in search of prey. From La Cruz del Condor lookout point (30 miles west of Chivay and 4,000 feet above the canyon floor), you can witness their solemn aerial ballet.

On the Peru-Bolivia border, Lake Titicaca is the world's highest commercially navigable lake (12,500 feet above sea level). At night, its star-littered sky has a hallucinatory clarity, and it's not surprising that the place is sacred to locals (according to legend, it is the birthplace of the Incas). The Uros islands were constructed from "totora" reeds by the Uros people so they could escape the Incas; today, a few hundred descendants still live on the islands. Take the hour-long boat ride from Puno to observe this unique way of life.

Perched so high that the ravaging conquistadors missed it, this ruined Incan city, once home to about 1,000 residents, was rediscovered in 1911 by Yale archaeologist Hiram Bingham. Today you can see the remains of palaces, baths, temples, and some 150 houses. Although many visit by train on a day trip from Cuzco, staying in the nearby town of Aguas Calientes (where the train terminates) enables you to visit outside of peak hours and avoid the crowds by taking a bus from town that runs regularly up to the ancient citadel. If you're a hardy hiker, you can reach the ruins via the arduous Inca Trail (a two- or four-day trek) or a day hike along the last stretch of the trail from Aguas Calientes. The ruins are open from dawn to dusk ($40). If you plan to visit Machu Picchu during the peak period of May through September, be sure to book well in advance (experts suggest three months), and with a tour operator. Only 2,000 hikers are permitted to start on the Inca Trail each day, a rule enforced by the Peruvian government.

Traced on the floor of the Nazca Valley are at least 10,000 mysterious lines and 300 different figures. Created by members of the pre-Inca Nazca culture (300 B.C.–A.D. 700), perhaps as a giant astronomical calendar to help predict rain, the menagerie includes a parrot, a whale, and "the Astronaut," a strange humanoid with its hand raised. Some figures are 1,000 feet long, while others are 100 feet wide and stretch for six miles. The best way to see the Nazca Lines is by plane. Several local operators offer the stomach-churning ride for about $50, or you can opt for a round-trip day flight from Lima over the lines with Aero Condor (51-1-614-6014; aerocondor.com.pe; $365).