While the main features of atomic nuclei are well described by nuclear mean-field models, there is a large and growing body of evidence which indicates an important additional role played by spatially-correlated nucleon-nucleon structures. The role of nucleonic structures was first suggested by Heidmann in 1950 to explain the pick-up reactions of energetic nucleons. Since then, a steady flux of new experimental evidence has confirmed the presence of similar structures inside atomic nuclei, dominated by correlations between pairs of nucleons. The role of these internal nucleon-nucleon correlations has been established using various energetic probes like photons, pions, leptons and hadrons. These correlated structures are essential for understanding the interaction of particles with nuclei and their presence provides an explanation of many specific nuclear phenomena, including backscattered protons, copious deuteron production, sub-threshold particle production, neutrino interactions with nuclei and the EMC effect. On the theoretical side, these measurements have stimulated a large number of phenomenological models specifically devised to address these enigmatic observations. While reviews exist for specific interactions, there is currently no published commentary which systematically encompasses the wide range of experimental signatures and theoretical frameworks developed thus far. The present review draws together the synergies between a wide range of different experimental and theoretical studies, summarises progress in this area and highlights outstanding issues for further study.