We demonstrate a general approach to characterize compositional heterogeneity in polymer thin films using Fourier transform infrared (FTIR) spectroscopy. Polymer films with varying degrees of heterogeneity were prepared using a model chemically amplified photoresist where a photoacid catalyzed reaction-diffusion process results in the formation of methacrylic acid (MAA) rich domains. Within these domains, the carboxylic acid groups dimerize through hydrogen bonding. FTIR measurements of the relative fraction of hydrogen-bonded vs free carboxylic groups are used to quantify the degree of compositional heterogeneity. The FTIR data from compositionally homogeneous systems, statistical copolymers, and polymer blends follow the expected linear dependence of the relative hydrogen-bonded fraction with composition. For the chemically amplified photoresist system, the FTIR data deviate substantially from that of the homogeneous distribution. Furthermore, parameters describing the size of the heterogeneity can be determined from a solid sphere model of the deprotected regions catalyzed by the diffusing photoacid. The degree of the spatial heterogeneity varies with changes in the photoacid concentration, reaction conditions, and initial copolymer composition. Increased nonreactive comonomer content decreases the degree of heterogeneity by reducing the hydrogen-bonding efficiency, which is consistent with the dilution of MAA groups.