Abstract The assumption of perfect periodicity in the crystal lattice is the most basic tenet of crystallography. However, many materials are not crystalline. Even when they are the atomic structure of real materials is often less than perfectly periodic, and usually deviations from perfect periodicity have significant effects on their properties. Thus in order to characterize the structure of real materials by diffraction the crystallographic approaches need to be complemented by other methods focusing on disorder. B. E. Warren was a pioneer of such alternative, non-crystallographic approaches, including the method of atomic pair-density function (PDF) analysis. With the advent of synchrotron based radiation sources, such as pulsed neutron sources and synchrotron radiation sources, it recently became possible to apply the PDF technique on crystals with and without disorder, covering the whole spectrum of structural order and disorder. Here some of the recent progresses in this approach made in my research group are reviewed.