Modern synchrotron beamlines often use standard techniques to eliminate harmonics from the beam. Use of an undulator gives sharp peaks and may avoid the corresponding harmonic. Most bending-magnet and wiggler beamlines use detuning of the second plane of the monochromator or an X-ray total reflection harmonic rejection mirror. Often the monochromator is, for example, monolithic Si(111) or Si(311) or Ge(111), and the second harmonic is forbidden. It is well known that these approaches do not fully eliminate harmonics, and in many cases a significant third harmonic remains in the beam at the sample, especially at lower X-ray energies. Harmonic components have completely different absorption and scattering coefficients to the main wavelength, which add baseline, noise and sometimes structure to the measurements. This prevents the direct measurement of absorption coefficients, which impacts the ability of theory to predict oscillation amplitudes and edge jumps. This chapter discusses the effect of harmonic contamination on transmission measurements.