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We have 2 friends joining me and my husband in Peru for the last 2.5 weeks of our trip. THe two major things we are saving for the end is the amazon and Machu Pichu/Cusco. We will be there mid to late May.

1) We want to use cusco as our base so it seems like we will be

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From Cusco, I did the Tambopata Reserve from Puerto Maldonado. I was only 30 minutes from Puerto Maldonado. In retrospect, I would have wanted to be deeper in the jungle.

If I could do it again, I would do the Manu Biosphere which is more difficult to access and further, but seems to be a more authentic jungle experience.

I also would have liked to be deeper in the jungle but it was a nice place to relax after the Inca trail. My advice is to fly from Cusco to the jungle. A bus trip is far too long and uncomfortable. Plus the airport in The Amazon is pretty interesting. Nothing like an xray machine that is not plugged in and the good old bag squeeze test to put your mind at ease for the flight home.

haha, i dont know why that was cut off...shoddy internet connection I suppose.

1) We will be using Cusco as our base so it seems like we want to find a way to get from Cusco to the jungle. SHould we venture out on our own, take a tour, etc? What are the prices like for the options. We are traveling with 2 science nuts so it would be nice for this to be educational for all. Should we do a tour or just organize with a lodge?What are our options close to Cusco?

2) We were plannning on doing the inca trail but were too late to buy tix in Jan. We want to hike, but nothing that intense since I think the altitute is getting to us more than we thought. What are our options as far as seeing Machu Pichu is concerned?

Thanks for the great advice so far! We are really stoked for Peru. It sounds like Manu is the way to go!

As for the jungle trip, as post #1 said, you'd probably go from Puerto Maldonado. The other option is Iquitos, but that is probably too far from Cuzco, and the only way to get there is by flight.
In your situation I'd arrange for a tour not before my arrival to Puerto Maldonado.

Re Inca trail - there are alternative trails. I walked Salkantay which I thought was even better, and I can really recommend it. I didn't need to book in advance, I did it after my arrival to Cuzco, and went on the trail two days later. I used the day in between for Sacred Valley tour.
Inca trail is too commercialized and therefore more expensive. It gets also too crowded at camp sites. It's a bit too much of a tourist pilgrimage. The other trails are not. Another trail you might consider is Lares. All of them lead to Aguas Calientes and Machu Picchu.

I'm assuming you're not in Peru yet. If not, you've got to think about altitude problem, when doing your planning. Cuzco is on 3400 m asl, and every normal person needs a couple of days to acclimatise to that altitude and the thin air.

Hey Guys, thanks for the great responses! How far did you guys get into the jungle, since you both said you wish you had gotten further into the jungle? Also, how much did you guys pay? about 800/person? that's what we're seeing if we want to get into the actual manu reserve.

we did find a good trip but it doesn't actually get into the preserve. it goes into MANU CLOUDFOREST OR PILCOPATA. the price difference is pretty big and we really can't afford to get into the park but could squeeze it if we absolutely had to. know what i mean?

So, 1) did you arrange it before you got there? 2) where did you guys go? town/park name? 3) how'd you get there? and 4) how much did you pay?

many many thanks!!!