The trail starts in Mollepata, a couple of hours away from Cuzco and ends in Santa Teresa or Hidroelectrica giving access to Aguas Calientes for Machu Picchu. The trek is not as popular as the overbooked Inca Trail but many find it just as beautiful.
You can do this trek by an organized trip through an agency in Cuzco. Shop around, no need to book in advance.
It is perfectly possible to do this trek alone if you have experience. You will have to spend at least one night at 3900 masl or above and you will need camping equipment good for freezing temperatures.
Bring some water purification pills. There are many streams, but also many animals around. Some travellers drink from the streams without purification, but it is better to be on the safe side.
You can rent a mule in Mollepata and other villages along the way.
You will need to carry food for at least two and a half days.
To get to Mollepata you can take a taxi (60 soles for the whole car) or take a shared minibus from Arcopata in Cuzco for 15-20 soles per person.
Apparently there is a fee for doing the trek. Read this article!!!! The first day of hiking from Mollepata to Soraypampa will be gently uphill and mostly along a road (there are a couple of places selling drinks and snacks). There are some shortcuts you can take to reach to Soraypampa where will probably be the highest and coldest place where you sleep on this trek. There is a campsite, but you can also wild camp in the bush.
Take it easy on the pass the next day, especially if you are not acclimatized.
There is an unmanned (free) campsite just after Huaracmachay when you start going down in the lush valley. You hit the first small shops in Chaullay and Collpampa.
A hot pot is being constructed at the hot springs (close to a bridge) after Collpampa so it is not possible to bathe at the moment (July 2013). At the hot springs you can cross the river and hike down on the left side of the valley (more interesting) or you can stay on the road on the right side of the valley. At La Playa (actually slightly further down) there is a pedestrian bridge where you can cross to the right side of the valley if you were hiking on the left side. There is a campsite for organized groups at Lucmabamba (near a school), but if you ask they will let you camp for free at the football field next to it and you can use their facilities. There are also shops around, where you can also buy pasta.
It is highly recommended (though more difficult) to hike from here to Hidroelectrica rather than to Sta Teresa. The trail to Hidroelectrica is very well marked. You will have to climb for 3 hours then go down for 2 hrs to reach Hidroelectrica. Some 15 minutes after the top of the climb there are some ruins with amazing views to Machu Picchu where you can wild camp. This is highly recommended if you can time it so. If you decide to explore the ruins, watch out for rattlesnakes and tarantulas on the overgrown paths around. The same is valid for the whole hike in that area.
From Hidroelectrica it is 2.5-3 hrs along the railway to reach Aguas Calientes.
Snakes, tarantulas - these avoid people as much as possible.
Use a lot of sun protection.
Bring some bug repellent.