For hiking from Cuzco and hikes in the Sacred Valley, you can take a tour with Kondor Path Tours. The Inca Trail is one exception: you must go with an agency. See the section on the Inca Trail and alternatives.
Choquequirao is becoming one of the most popular treks in the region. The town, which sits more than two miles above the Apurimac Gorge, was discovered by Hiram Bingham just before he stumbled upon Machu Picchu, then eventually lost it again. The five-day/ four-night trek passes by snow-covered mountain peaks and glaciers, the high jungle, little-known Incan buildings and ruins, and raging rivers. There are several locations on the trip where there is an excellent chance to see the giant Andean condor.
A five- to seven-day circuit takes you to the area’s highest peak, Ausangate (6,384 m/20,939 feet). The trip takes you to grasslands filled with herds of alpacas and small rural villages that have changed little since Incan times.
The trek starts from the town of Tinqui, which is a 04-hour drive from Cuzco. Ausangate is the site of Qoyllority, the snow star festival held every May or June, which features a midnight trek to the glacier by thousands of Andean peoples. Other expeditions from Tinqui lead to Laguna Sibinacocha (seven-eight days) and Pitumarca (six days).
The way to Vilcabamba is not necessarily through Cuzco, but you must organize the trip from here. The mountain hideout was the last stronghold of the Incas until what killed Manco Inca here in 1544. It is what explorer Hiram Bingham was looking for and thought he had found when he discovered Machu Picchu. Also known as Espiritu Pampa, the ruins are 70 km/ 42 miles from the lowland town of Quillabamba. It has yet to be excavated on a large scale, so much of it is in pieces and overgrown. To visit here, one must hike for about a week round-trip.