Polarized synchrotron-based attenuated total-reflection infrared (ATR–IR) spectra of crystals of natural zircon of various origins and degree of disorder are reported. We demonstrate the potential of ATR–IR microspectroscopy for non-destructive structural analysis of zircon microcrystals. Disorder-related IR absorption at wavenumbers lower than the bands arising from the fundamental A2u[ν3(SiO4)] and Eu[ν3(SiO4)] zircon modes was observed, which reveals the existence of spatial regions with abundant SiO4 tetrahedra with longer bonds. A pronounced peak near 990 cm−1 is indicative of an abundance of polymerized SiO4 tetrahedra. Weak signals in the range 1050–1250 cm−1 show connectivity defects (broken Si–O–Zr bridges) and the existence of shorter Si–O bonds.