Although it's possible to see a bit of the jungle on a day tour from Puerto Maldonado or Iquitos, exploring the Amazon Basin on your own isn't recommended because the areas that you could reach tend to have degraded forest and few animals. If you want to see rainforest wildlife, book a tour with a company that owns one or more lodges located in remote, wild areas.
Amazon Conservation Association. This respected conservation organization (with offices based in the U.S.) protects vast expanses of tropical wilderness and has three biological research stations in pristine, private reserves near the Manu Biosphere Reserve or Tambopata National Reserve that few people visit. In recent years, the organization has built bungalows and begun operating tours that visit one or more research stations on 5- to 10-day trips that begin in either Cusco or Puerto Maldonado. Those tours offer excellent bird-watching and other wildlife encounters, and the profits support conservation. 1012 14th Street NW, Washington, District of Columbia. 202/871–3777; birding.amazonconservation.org. From $507.
InkaNatura Travel. InkaNatura Travel runs 1- to 11-night nature tours to the Manu Biosphere Reserve or the Tambopata National Reserve with overnight stays at any of six nature lodges. These lodges are in some of the most pristine areas that travelers can visit in Peru, so the company's tours offer some of the best exposure to the wildlife of the Amazon Basin available anywhere. It has tours to both Manu and Tambopata out of Puerto Maldonado. 971/427–346; www.inkanatura.com. From $363 per person.