A rigorous analysis confirmed by experimental results is presented for attenuated total reflectance, Fourier-transform infrared (FTIR-ATR) spectroscopy applied to the study of small molecule diffusion in polymers. FTIR-ATR Fickian diffusion models are derived for a constant surface concentration and for an adjacent mass-transfer boundary layer. An FTIR-ATR Case II transport model demonstrates the ability to discriminate between transport modes. New experimental results for the acetone-polypropylene, methanol-polystyrene and methanol-poly(methyl methacrylate) systems are consistent with gravimetric sorption and nuclear magnetic resonance measurements. An important result is the detection of multiple hydroxyl peaks for methanol during diffusion, indicating different hydrogen bonding states and the calculation of separate diffusion coefficients for each state in polystyrene.