© 2017 IOP Publishing Ltd. Molecular dynamics (MD) simulations are performed to investigate the production of point defects in α-quartz by oxygen and silicon primary knock-on atoms (PKAs) of 0.25-2 keV. The Wigner-Seitz (WS) defect analysis is used to identify the produced vacancies, interstitials, and antisites, and the coordination defect analysis is used to identify the under and over-coordinated oxygen and silicon atoms. The defects at the end of the ballistic phase and the residual defects, after annealing, increase with increased PKA energy, and are statistically the same for the oxygen and silicon PKAs. The WS defect analysis results show that the numbers of the oxygen vacancies and interstitials (V O , O i ) at the end of the ballistic phase is the highest, followed closely by those of the silicon vacancies and interstitials (V Si , Si i ). The number of the residual oxygen and silicon vacancies and interstitials are statistically the same. In addition, the under-coordinated O I and Si III , which are the primary defects during the ballistic phase, have high annealing efficiencies (>89%). The overcoordinated defects of O III and Si V , which are not nearly as abundant in the ballistic phase, have much lower annealing efficiencies (<63%) that decrease with increased PKA energy.