Oxidized carbon nanotubes (CNTs), which can form a stable homogeneous suspension in water close to a solution phase, were synthesized and used for matrix-assisted desorption/ionization mass spectrometric (MALDI-MS) analysis of biomolecules. Infrared (IR) spectra, transmission electron microscopy (TEM) and particle size analysis were used for the characterization of the oxidized CNTs. The results indicate that the physical structure of the CNTs was not damaged, but carboxylate groups were introduced onto the surface of the CNTs. In addition, impurities including amorphous carbon, which is one of the main reasons for ion source contamination, were destroyed by the oxidization. The carboxyl groups on the oxidized surface of the CNTs can not only provide an additional proton source, but can also increase the surface polarity and solubility of the CNTs, making it easier to manipulate which is important for MALDI analysis of some biomolecules, especially larger peptides and proteins. The oxidized CNTs were successfully applied to the analysis of neutral oligosaccharides, peptides, and insulin, and thus promise to be an efficient matrix for MALDI-MS analysis of biomolecules. Copyright © 2004 John Wiley & Sons, Ltd.