Recent data on He diffusion challenge the temperature sensitivity of apatite (U–Th)/He thermochronology: the damage induced by recoil of U and Th decay series during emission of α particles (α-recoil damage) has been proposed to modify He-diffusion properties through time. However, we propose that annealing of these irradiation defects may be an important phenomenon and may be significant in case of slowly-cooled or reheated basement rocks. To test this hypothesis, we developed a quantitative model including an explicit treatment of α-recoil damage, annealing, and their effect on He-diffusion kinetics, and calibrate it against literature data. Our model is based on two hypotheses: (1) helium is in equilibrium between an apatite crystal and its defects and (2) alpha-recoil damage annealing can be described analogously to fission-track annealing. This model has been embedded into a Monte Carlo simulation of helium production/ejection/diffusion and applied to data from the French Massif Central; a complex slowly-cooled terrain with burial reheating, where the thermal history has been constrained by previous fission-track (FT) data including FT length distributions. (U–Th)/He ages are close to the FT ages from the same samples and are generally reproducible among replicates, but some samples present He-age dispersion that is not correlated with crystal size. Our model reproduces the Massif Central data very well except for three samples where He ages are older than corresponding FT ages. We show that annealing of irradiation damage has an important impact on retentivity of helium and that the He content, [He] is only a rough approximation of the damage level. In particular our results show that independence of He ages on crystal sizes, in case of reheated samples, is a clear indication of the higher He retentivity induced by α-recoil defects and that an explicit treatment of defect annealing is required for a correct interpretation of (U–Th)/He ages in such a case. More generally a correlation with the crystal size can bring information on the thermal path only if the age of defects, well represented by the fission-track age, is available, due to the dependence of the partial retention zone on damages. Conversely, in case of rapid cooling or for samples having low U and Th contents, damage effects can be ignored without significant effects on He ages.