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One of the major drawbacks associated with in situ pyrometry is the fact that the sample emissivity is unknown. Real-time in situ measurements of HgCdTe growth temperature are made even more difficult by the change in emissivity that takes place during deposition. In this article, a Fourier transform infrared spectrometer was utilized to measure simultaneously the sample emission and its emissivity, thereby making it possible to determine the sample temperature at any growth stage. Two different methods of temperature determination from the spectral radiance were compared, and applied to the in situ monitoring of the growth of a HgCdTe/CdTe(211)B/Si(211) heterostructure. A computer simulation of the measuring procedure showed that the technique is very sensitive to signal reduction resulting from beam misalignment and/or imperfect calibration of the detector spectral response. © 2001 American Vacuum Society.