Scanning transmission x-ray microscopy ͑STXM͒ has been used to study isolated carbon nanotubes for the first time. STXM and transmission electron microscopy were applied to the same type of nanotubes, providing unique information about their composition, and electronic and structural properties. The carbon 1s near-edge x-ray absorption fine structure spectra show significant differences between multiwall carbon nanotube and carbon nanoparticle contaminants. Pristine and acid treated multiwall carbon nanotubes were also compared, highlighting the potential of the technique to differentiate surface functional groups at the nanoscale.