This 21-day tour brings together most of the main travel routes throughout Peru, and travelers can easily take one part (for instance the journey from Lima to Cusco) and take out another (the tour of northern Peru). More than anything, it is proof of all that Peru has to offer—and it still leaves out a lot.
The odyssey unfolds chronologically among Peru’s ancient ruins and colonial cities, with a dab of Amazon and a dash through the desert for balance. Getting around is accomplished via a straightforward combination of planes, trains, buses, and combis.
In the morning see Trujillo’s Museo Cassinelli , then hop on a bus for Chiclayo  (three hours). Hire a private car and head to a country inn at Túcume  (45 minutes), where you will stay two nights sleeping in the bucolic countryside near the pyramids.
Fly from Chiclayo to Lima. Here you begin the the time-honored backpacker’s route to Cusco . Take a bus to Pisco (three hours) and a short combi ride to the beach town of Paracas, where you stay two nights.
Explore Reserva Nacional de Paracas. Watch sea lions and perhaps endangered Humboldt penguins, picnic on a wilderness beach, and return to your hotel for sunset over the Pacific Ocean.
Take a bus to Nasca (2.5 hours) to visit Museo Antonini and aqueducts and stay the night. Or take a bus to Ica (one hour) for a tour of pisco bodegas and sandboarding on the dunes above Lago Huacachina, where you stay the night. You choose.
Enjoy a morning overflight of the Nasca Lines from either Nasca or Ica. Take the bus to Arequipa from Ica (eight hours) or Nasca (6.5 hours). Check in for a two-night stay in Arequipa.
Take a flight or bus trip from Arequipa to Puno  (seven hours by bus).
Continue onward to Cusco . From Puno you can either fly, take a direct nonstop train, or a ride tour bus that allows you to see the ruins along the way (nine hours). Upon arrival, grab a 1.5-hour taxi or combi ride from Cusco to Ollantaytambo , a living Inca village in the heart of Peru’s Sacred Valley .
Recharge in the lush surroundings of the Sacred Valley. Options include touring Ollantaytambo’s old Inca city  and the Temple of the Sun , rafting the Río Urubamba, and going horseback riding or day hiking on one of the area’s many Inca trails. On the second day, walk or mountain bike from the Inca ruins of Moray down a steep valley past the Salineras , or salt mines, and back to Ollantaytambo.
Take an early morning train to Machu Picchu  from the Sacred Valley and cruise to the ruins as early as you can. Spend a full day at Machu Picchu, then hop on the afternoon train-and-bus combination back to Cusco.
From Puerto Maldonado catch a morning flight to Lima ’s airport, where you can leave your bags, and then take a quick peek at the city center and enjoy a gourmet dinner in Miraflores . Then hop a red-eye for home.