Because both Cusco  and Machu Picchu  are near the Amazon , we have designed this 10-day travel itinerary to take you to Peru’s most important cultural ruins and allow you to see highlands, cloud forest, and rainforest.
Depending on your interests or travel dates, you might want to consider modifications to this itinerary. Between October and April when the jungle near Puerto Maldonado is rainy and many of its lodges are closed, fly from Lima  to Iquitos  instead and visit the Reserva Nacional Pacaya Samiria .
An option in the Puerto Maldonado region that offers a chance to see biodiversity similar to that of Manu and Pacaya Samiria is the Tambopata Research Center , a seven-hour boat ride from Puerto Maldonado.
Arrive in Lima  and catch an early morning connecting flight to Cusco . In Cusco, take a taxi to Ollantaytambo , a living Inca village in the Sacred Valley , where you can rest and acclimatize.
Tour the Sacred Valley, with stops at the Ollantaytambo Temple of the Sun  and the market  and ruins of Pisac . On day three, explore the village of Chinchero  before hiking or mountain biking from the enigmatic circular Inca terraces at Moray  past the crystallized salt mines known as Salineras and back to Ollantaytambo.
Take the early morning train to Machu Picchu  and spend the day touring the ruins and bird-watching in the cloud forest. Return on the afternoon train-and-bus combination to Cusco , where you will spend two nights.
Experience Cusco’s unique combination of Inca ruins, colonial architecture and museums, markets, and cafés.
If you choose to go to the Manu Biosphere Reserve , you will fly from Cusco into Boca Manu. Upon arrival, you will take a motorboat ride into the Manu Biosphere Reserve and settle into your jungle lodge or tented camp.
Hire one of the many Manu agencies  and tour an oxbow lake on a platform boat equipped with a spotting scope. Manu’s oxbow lakes host a huge range of wildlife, including giant otters, 13 species of monkeys, and large mammals like tapirs. Hike through different areas of local rainforest with a guide who along the way points out wildlife that you would otherwise miss. Explore the jungle canopy by climbing up to a lookout tower 20 meters above the forest floor.
Return to Boca Manu by boat. Catch the 35-minute flight from Boca Manu back to Cusco , flying over jungle, highlands, and glacier-capped mountains along the way. Catch a connecting flight into Lima  and arrive in the early afternoon. Head to central Lima to see the Catedral and Palacio del Gobierno , and have lunch at T’anta , all on the Plaza Mayor. Return to the airport for a night flight home.