The Southern Sierra region of Peru is characterized by high mountains and steep, deep valleys. Many roads are unpaved. Thus, travelling is often somewhat troublesome and slow, but the scenery is amazing.
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You can fly between Cusco and Ayacucho, but the most common method of travel in this region is by bus.
Hiking: See Inca Trail, Machu Picchu, Choquequirao, and Colca Canyon.
Into the jungle (2-3 nights) - If you're game, fly to one of the following two lodges between Days 1 and 2, because anything after Machu Picchu is sure to be a letdown. Pack one bag and leave in Cusco what you don't need. The Manu Wildlife Center, owned by a nonprofit environmental conservation group, has the most creatures but fewer comforts. If you want a taste of the jungle in an elegant setting, go to Reserva Amazónica. The surrounding cattle ranches mean fewer wild animals, but the huts are plusher and there's a masseuse. Reserva is also a better option if you have only two nights (although three is ideal in either location) because the 30-minute charter flights to Manu are highly undependable. Reserva also offers community visits, which Manu doesn't. Wherever you land, take part in as many outings as you can.
Urubamba Weavers' Route Trek (2 nights) - The classic Inca Trail was the primary route between Cusco and Machu Picchu, but the Incas traversed hundreds of other paths, and you can as well. Instead of catching the train to Machu Picchu on Day 3, drive to the trailhead of the Urubamba Weavers' Route. This hike from Ollantaytambo to Lares takes you through villages unchanged for centuries. The first camp lies in the shadow of Terijuay. The middle of Day 2 marks the high point of the trek, literally — — after which a gradual descent leads through potato fields and into the tiny village of Cochayoq. Midway through Day 3, the trek reaches Lares and then you are returned to the Sol y Luna Lodge & Spa. It is recommended that you purchase the services of a trekking company for this hike since it is at such a high altitude. This is a moderate-to-strenuous trek, with four to six hours of hiking on each of three days and recommended for experienced hikers only. Although the spongy moss underfoot makes this a relatively low-impact route-the Inca Trail, in comparison, is paved with stones-the altitude is a challenge. If you do have trouble, you can always take a hit of oxygen from your guide's canister or jump on the "ambulance horse." If serious symptoms persist, getting to a lower altitude is essential.