A thermocouple‐instrumented wafer was used to monitor the wafer temperature during chemical vapor deposition of a polycrystalline‐silicon layer in a lamp‐heated rapid thermal processor. The temperature of the oxidized silicon substrate varies by more than 100 °C as the polycrystalline‐silicon layer is deposited because the reflectivity of the sample changes with increasing thickness of the deposited layer. Cross‐section transmission electron microscopy shows that when the temperature decreases below the polycrystalline‐to‐amorphous transition temperature during deposition, a phase change occurs in the structure of the deposited film. The change in temperature qualitatively corresponds to the change in reflectivity as a function of silicon film thickness calculated from a simple model.