Modern infrared (IR) spectroscopy and imaging has a wide range of applications in health and plant sciences. Initially, it was extensively used for the study of proteins, nucleotides, lipids and carbohydrates. With time, its use has extended to disease assessment to discriminate healthy and diseased samples on the basis of chemical changes. The application of an advanced focal plane array detector, which is able to scan a large area of samples in a short time, helps in investigating specific changes that could be correlated with different environmental stresses. An IR microscope connected with a synchrotron light source further enhances the lateral spatial resolution at diffraction limit because of the compact beam size. For example, synchrotron-based IR spectroscopy imaging in combination with multivariate statistical analysis has been proven to be a powerful non-destructive analytical tool to probe changes in plant cell wall composition/structure in response to biological processes and environmental stresses. New development of nano-Fourier transform infrared spectroscopy (FTIR) combined with scattering type scanning near-field optical microscopy breaks the diffraction limitation, which opens the new area of applications. This review focuses on a new area of diagnostic research as well as development of IR spectroscopy and imaging for biological specimens including compositional changes in plant cell wall.