This odyssey through Peru’s northern highlands and Amazon  is for those who want to get off the beaten path to experience an awesome cross-section of Peru’s geography.
If you have a few extra days, consider starting in either Trujillo  or Chiclayo . These cities are close to an array of pre-Inca ruins and their corresponding museums. The most ambitious idea is to fly to Chiclayo  first to visit Museo Tumbas Reales de Sipán  and Túcume . Then take a three-hour bus ride to visit Trujillo, along with the ruins of Huaca de la Luna  and Chan Chan . From there you would head to Cajamarca and follow the trip described here.
However, if you want to spend extra time in virgin rainforest, you should explore the Reserva Nacional Pacaya Samiria . Get off the Yurimaguas–Iquitos cargo boat  in the middle of the first night at the town of Lagunas. From here, you can head out with a dugout canoe and a guide for a week of camping in the reserve.
Arrive in Lima , and then fly to Cajamarca, where Francisco Pizarro captured Inca emperor Atahualpa and ransomed him for a room of gold. Besides Atahualpa’s chamber (called the Cuarto de Rescate), Cajamarca offers baroque churches, the carved aqueducts at Cumbemayo, and a stunning pastoral setting.
After a morning visit to Cumbemayo, begin the rough overland journey to the cloud forest of the Chachapoya. The first leg of the trip involves an afternoon bus from Cajamarca to the charming country town of Celendín (four hours). There you will spend the night before heading to Leymebamba in the morning.
Take a bus to Leymebamba. This is a spectacular, eight-hour journey down and up the Marañón Canyon, which is deeper than Arizona’s Grand Canyon and ranges from high-altitude grasslands to the subtropical valley floor. Overnight in a hotel near Leymebamba’s quiet central plaza.
Explore Leymebamba with a visit to the Museo Leymebamba and a hike to the lost city of La Congona. That afternoon, take a colectivo down the Utcubamba Valley to Chillo or Tingo (1.5 hours). Plan on a two-night stay at one of the charming country lodges at the foot of Kuélap.
Hike to the Chachapoya citadel of Kuélap.
Take a colectivo to Pedro Ruiz (one hour) to get back on paved highway, and hop on a bus for Tarapoto  (eight hours).
The most adventurous part of this trip begins with an early-morning colectivo ride over the muddy, potholed road to Yurimaguas  (6–8 hours). That afternoon, board a cargo boat down the Río Huallaga for a 36-hour ride bound for Iquitos .
Rest up on the boat by swinging on a hammock, eating bananas, and watching the Amazon float by.
Rise early both days to catch sight of hoatzins and river otters at their early morning feeding. In the afternoon, wander the terra firma in search of tiny frogs or fish for pirañas.
Return to Iquitos  for a celebratory dinner—or keep floating on into Brazil!
Fly to Lima  and return home.