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The evolution of point defect concentrations under irradiation is controlled by their diffusion properties, and by their formation and elimination mechanisms. The latter include the mutual recombination of vacancies and interstitials, and the elimination of point defects at sinks. We show here that the modelling of this evolution by means of atomistic kinetic Monte Carlo (AKMC) simulations, necessarily using small system sizes, introduces strong space and time correlations between the vacancies and interstitials, which may strongly affect the recombination rate and the point defect concentrations. In such situations, standard rate theory models fail to predict the actual point defect concentrations. The effect is especially strong when the elimination of point defects occurs only by recombination, but can still be significant in the presence of sinks. We propose a new Correlated Pair Theory that fully takes into account the correlations between vacancy and interstitial pairs and predicts point defect concentrations in good agreement with AKMC simulations, even in very small systems. The Correlated Pair Theory can be used to modify the elimination rates in AKMC simulations to yield point defect concentrations as predicted by the standard rate theory, i.e. representative of large systems, even when using small simulation boxes.