The very term “Fourier transform infrared spectroscopy” (FTIR) has become obsolete because there are now no research-quality non-Fourier transform (dispersive) mid-infrared spectrometers being manufactured commercially. Fundamental differences between an FTIR spectrometer and a dispersive-IR spectrometer go well beyond the mere convenience of having data in digital format. The way in which an FTIR spectrometer records a spectrum must be understood to set the optimum data collection parameters for a particular sample. There is no one combination of instrument, data collection parameters, and sampling device that will provide the best possible signal-to-noise ratio (S/N) throughout the infrared spectrum. A typical sample of a submillimolar protein solution in water pushes the limits of the instrument because of the dilute analyte and the high absorbance due to water. The optimum sample path length, detector, detector amplifier gain, and data sampling rate will depend on a region of the spectrum. This chapter discusses the basics of Fourier transform spectroscopy and spectrometers that are important in obtaining the highest S/N in a spectrum of an aqueous biological sample. This chapter discusses and illustrates some of the sampling devices and techniques that have been successfully used for aqueous protein FTIR studies. © 1993, Academic Press, Inc.