The microhydration effects on two polymer electrolyte membrane materials, Nafion and bis[(perfluoroalkyl)sulfonyl] imide (PFSI), were investigated by analyzing optimized geometries and normal modes of vibration. The calculations were performed on periodic structural models with systematic increases of the number of water molecules around the polar head groups. A strong effect of microhydration on the structure of the polar head groups was observed due to a large red shift of the SO-H (Nafion) and N-H (PFSI) stretching modes of about 600-1000 cm-1. In addition, frequency calculations showed how H2O stretching vibrations contribute to the overall high frequency vibrational spectra. Both asymmetric and symmetric stretching modes of the SO2 group (νas(SO2) and νs(SO2)) were red-shifted indicating the S-O bond weakening upon microhydration. PFSI models showed spectral changes upon microhydration comparable to those observed for Nafion. However, distinct spectral features related to the differences in the polar head groups were observed. Lower N-H stretching frequency compared to the SO-H mode explained a stronger acid character of the PFSI polar headgroup and its earlier proton transfer ability (less water molecules needed for the proton release).