The IRμs™ is the first fully integrated system for Fourier transform infrared (FT-IR) microscopy. FT-IR microscopy combines light microscopy for morphological examination with infrared spectroscopy for chemical identification of microscopic samples or domains. Because the IRμs system is a new tool for molecular microanalysis, its optical, mechanical and system design are described to illustrate the state of development of molecular microanalysis. Applications of infrared microspectroscopy are reviewed by Messerschmidt and Harthcock.Infrared spectral analysis of microscopic samples is not a new idea, it dates back to 1949, with the first commercial instrument being offered by Perkin-Elmer Co. Inc. in 1953. These early efforts showed promise but failed the test of practically. It was not until the advances in computer science were applied did infrared microspectroscopy emerge as a useful technique. Microscopes designed as accessories for Fourier transform infrared spectrometers have been commercially available since 1983. These accessory microscopes provide the best means for analytical spectroscopists to analyze microscopic samples, while not interfering with the FT-IR spectrometer’s normal functions.