The infrared beam on both the main Nicolet Nexus bench and the attached Spectra-Tech Continuum microscope has been shown to be partially polarized. The degree of polarization is approximately 30%. Although the state of polarization of the infrared beam is of no consequence when measuring the spectra of isotropic materials (gases, liquids), there is a potential problem when considering the spectra of anisotropic materials. Single band intensities are particularly prone to error as small changes in sample thickness or orientation directly affect the intensity. Thickness effects can be overcome by measuring intensity ratios. However, because of the partially polarized nature of the infrared beam, even intensity ratios, illustrated here by the ratio amide I/II of collagen fibres, vary with sample orientation. If overlooked, this effect can be problematic when measuring infrared spectra with an FTIR microscope from samples that are anisotropic or contain anisotropic domains, even though they may appear isotropic on a macroscopic scale. Because dichroic ratios remain unaffected, the intensity ratio from two bands with different transition moments may be used to give a strong indication of the orientation of the sample. This work is illustrated by reference to the FTIR spectra of orientated polyethylene, collagen tape and human trabecular bone.