Ion-induced damage on organic materials has been evaluated with secondary ion mass spectrometry. However, conventional sputtering beams such as SF5+ and C60+ cannot etch organic materials without inducing damage, and evaluating the damage depth distribution in these materials is difficult. Large gas cluster ions can etch organic materials without damage, and in this study, the damaged layer thickness was evaluated by molecular depth profiling with Ar cluster ion beam. The characteristic molecular ions were not detected in the spectra after etching with Ar monomer beam, indicating that the chemical structures of phenyl-C61-butyric acid methyl ester (PCBM) and polystyrene (PS) were seriously damaged. The intensity of the fullerene molecular ion reached a peak at the depth of about 35 nm. For PS, the peak intensity of m/z 91 increased with sputtering depth and saturated at about 45 nm. These values agreed with the projection range of Ar+ in PCBM and PS, respectively. These results indicate that the ion-induced damage depth was the same as the projection range of its ion. Copyright © 2012 John Wiley & Sons, Ltd.