Combining high resolution scanning tunneling microscopy and first principles calculations, we identified the major native defects, in particular the Se vacancies and Se interstitial defects, that are responsible for the bulk conduction and nanoscale potential fluctuations in single crystals of archetypal topological insulator Bi_{2}Se_{3}. Here it is established that the defect concentrations in Bi_{2}Se_{3} are far above the thermodynamic limit, and that the growth kinetics dominate the observed defect concentrations. Furthermore, through careful control of the synthesis, our tunneling spectroscopy suggests that our best samples are approaching the intrinsic limit with the Fermi level inside the band gap without introducing extrinsic dopants.