Paramagnetic defect centres and their relation to variable types of colouration were studied for eleven natural zircon crystals from three localities in North Carolina (USA), Massif Central (France), and Ural Mountains (Russia) using electron paramagnetic resonance (EPR) and optical absorption spectroscopy. The presence of tetragonal centres of trivalent rare-earth elements (REE3+) and niobium (Nb4+) irrespective of the colouration type and also in colourless grains suggests that these defects are not directly related to any specific zircon colouration. In contrast, the occurrence of two hole centres in crystals from North Carolina and the Massif Central correlates with the formation of specific broad bands in the absorption spectra. The appearance of pink colouration corresponds to the occurrence of a hole located at an oxygen nearest to Y3+ on zirconium site. This defect displays a single line at g = 2.006 in the EPR spectra for external magnetic field orientations parallel to the tetragonal crystal axis c. The related broad band in the optical absorption spectra peaks at 340–350 nm and its low-energy wing extends into the visible range. Reddish colour results from an intense broad absorption feature around 510–515 nm caused by a hole located at an oxygen next nearest to Y3+ substituting for Zr4+. A single line at g = 2.011 related to this “red” hole centre is observed in the EPR spectra in magnetic field orientation parallel c. The nature of the two paramagnetic centres was verified by their angular dependencies. Reddish-brownish and orange colour of zircon may appear for certain intensity relations between the two absorption bands with possible additional influence from charge transfer bands caused by Tb4+ centres. Yellowish-brownish colouration of zircon from the Ural Mountains is essentially different in nature. Several other paramagnetic defects with spin S = 1/2 were found in zircon from this locality besides the “red” hole centre, Tb4+, and REE3+ defects. There is a characteristic set of four bands in the optical absorption spectra. Additional heating and irradiation experiments are necessary for a correct assignment of paramagnetic defects to specific colour centres in this case.