This paper shows an actual overview of Science Technology and Innovation politics in Brasil, Colombia and Peru remarking its achievements and uncertainty, but also consequences and potential risks for the Amazon region. Another purpose is to compare this situation with the performance of academic and scientific institutions placed in the Amazon region and its borders, the installed capacity, background and limitations in academic cooperation with border neighbors. Finally, the article includes a proposal to discuss and design a partnership schedule of research and academic programs from and for the amazon borderlands.