Thermal cross-linking is widely used to impart stability or improved mechanical properties to layer-by-layer (LbL) assemblies. However, the kinetics of thermal cross-linking within LbL films is not well understood. Furthermore, because LbL films are generally ultrathin (<100 nm), the influence of confinement on cross-linking kinetics is potentially substantial. Using temperature-controlled ellipsometry, differential scanning calorimetry, and thermal gravimetric analysis, we are able to accurately track amide cross-linking within poly(allylamine hydrochloride)/poly(acrylic acid) LbL films. The rate of amidation is strongly influenced by film thickness and surface chemistry, which indicates that the observed "confinement effects" are primarily related to the catalytic contribution of hydroxyl groups present on the substrate's surface. The analytical techniques presented herein highlight new ways to access thermochemical information within ultrathin LbL assemblies.