The transition-metal dichalcogenide 1T-TiSe2 is a quasi-two-dimensional layered material with a charge density wave (CDW) transition temperature of TCDW ≈ 200 K. Self-doping effects for crystals grown at different temperatures introduce structural defects, modify the temperature-dependent resistivity, and strongly perturbate the CDW phase. Here, we study the structural and doping nature of such native defects combining scanning tunneling microscopy or spectroscopy and ab initio calculations. The dominant native single atom dopants we identify in our single crystals are intercalated Ti atoms, Se vacancies, and Se substitutions by residual iodine and oxygen.