In order to evaluate the impurity levels in carbon nanotubes, single walled carbon nanotubes (SWCNT) grown by the high pressure carbon monoxide process (HiPCO), SWCNT synthesized by a direct-current arc-discharge method in He gas with Fe/Ni/S catalysis and multiwalled carbon nanotubes (MWCNT) formed on a substrate of Ni–Cr–Fe alloy by thermal chemical vapor deposition are mass analyzed at atomic level by utilizing the unique capability of the scanning atom probe. Since the largest number of ions detected from the analyzed CNTs is C2+ and C+/C22+ is the second largest, the binding between carbon atoms is uniform and nondirectional. No metal ions except sodium ions are detected from the HiPCO SWCNT. Hydrogen ions detected from the HiPCO SWCNT is significantly smaller than two other CNTs. Metal ions detected from the dc arc SWCNT and MWCNT are localized in a range of a few nanometers.