The presence of defects in carbon nanotubes strongly modifies their electrical, mechanical, and chemical properties. It was long thought undesirable, but recent experiments have shown that introduction of structural defects using ion or electron irradiation can lead to novel nanodevices. We demonstrate a method for detecting and quantifying point defect density in individual carbon nanotubes (CNTs) based on measuring the polarization dependence (linear dichroism) of the C 1s → π* transition at specific locations along individual CNTs with a scanning transmission X-ray microscope (STXM). We show that STXM can be used to probe defect density in individual CNTs with high spatial resolution. The quantitative relationship between ion dose, nanotube diameter, and defect density was explored by purposely irradiating selected sections of nanotubes with kiloelectronvolt (keV) Ga ions. Our results establish polarization-dependent X-ray microscopy as a new and very powerful characterization technique for carbon nanotubes and other anisotropic nanostructures.