Molecular depth profiling of polymers by secondary ion mass spectrometry (SIMS) has focused on the use of polyatomic primary ions due to their low penetration depth and high damage removal rates in some polymers. This study is the third in a series of systematic characterizations of the effect of polymer chemistry on degradation under polyatomic primary ion bombardment. In this study, time-of-flight SIMS (ToF-SIMS) was used to assess 5 keV SF5+-induced damage of ∼90 nm thick spin-cast poly(2-hydroxyethyl methacrylate) (PHEMA) and ∼130 nm thick trifluoroacetic anhydride-derivatized PHEMA (TFAA-PHEMA) films. The degradation of these polymers under extended SF5+ bombardment (∼2 × 1014 ions cm−2) was compared to determine the effect of the pendant group chemistry on their degradation. The sputter rate and ion-induced damage accumulation rate of PHEMA were similar to a poly(n-alkyl methacrylate) of similar pendant group length, suggesting that the addition of a terminal hydroxyl group to the alkyl pendant group does not markedly change the stability of poly(n-alkyl methacrylates) under SF5+ bombardment. The sputter rate and ion-induced damage accumulation rate of TFAA-PHEMA were much higher than a poly(n-alkyl methacrylate) of similar pendant group length, suggesting that derivatization of the terminal hydroxyl group can significantly reduce degradation of the polymer under SF5+ bombardment. This result is in good agreement with the literature on the thermal and radiation-induced degradation of fluorinated poly(alkyl methacrylates), which suggests that the electron-withdrawing fluorinated pendant group increases the probability of depolymerization. Copyright © 2004 John Wiley & Sons, Ltd.