Over the last decade the use of synchrotron infrared microspectroscopy to spatially discriminate chemical and structural features in many different types of materials has grown considerably and has made significant impact in numerous research areas, in particular, in biological sciences and medicine. Although the brightness advantage of the synchrotron infrared (IR) source is well accepted as the key to high spatial discrimination, little attention has been given to measure the polarization properties of the synchrotron light at the sample stage in IR microscopy. In this work the intrinsic polarization of the IR source and its consequences for the study of anisotropic materials are discussed. The polarization characteristics of predominantly bending magnet radiation and predominantly edge radiation sources were measured at the microscope focus and compared. To illustrate the direct use of the intrinsic polarization of these sources in microscopy, the orientation and conformational details of a drawn polymer sample are considered.