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/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.