Abstract The present work aims at predicting at the atomic scale, binding energies of vacancies to vacancy clusters in zirconium, preparing this way the modelling of their growth. Empirical laws established on the basis of simulation results are suggested, describing the size dependence of formation and binding energies of small voids (involving up to 1000 atoms) as well as basal, prismatic and pyramidal vacancy loops involving the same number of vacancies. The detailed atomic configurations of the loops are examined and characterized by means of areas where atoms are mis-coordinated and by strain fields. The importance of mis-coordinated areas is emphasized by an examination of self-interstitial atom (SIA) diffusion mechanisms in the vicinity of basal vacancy loops. The loops act as sinks for SIAs that, depending on the temperature, migrate one- or three-dimensionally to the mis-coordinated areas from which they cannot escape. By this mechanism, the annihilation of vacancy loops by SIA absorption is inhibited.