Endogenous and oxidatively induced DNA damage, as evaluated by the comet assay, are widely used as biomarkers of oxidative stress in numerous dietary intervention studies. This analysis can be performed on fresh peripheral blood mononuclear cells (PBMCs) or on cryopreserved cells. However, information pertaining to the effects of cryopreservation on DNA damage is often missing, and this may be crucial in studies in which samples are analysed before and after intervention. The purpose of this study was to compare DNA damage in fresh versus cryopreserved PBMCs obtained from subjects following a 6-week intervention with wild blueberry drink or placebo drink. Fresh and 12-month-stored PBMCs were analysed for formamidopyrimidine-DNA glycosylase (FPG)-sensitive sites and H2O2-induced DNA damage. The levels of FPG-sensitive sites were significantly higher in the cryopreserved compared with the fresh cells (P < 0.001), while H2O2-induced DNA damage was significantly lower after storage (P < 0.001). Both the fresh and cryopreserved samples showed reductions in FPG-sensitive sites following the wild blueberry treatment (fresh PBMCs: from 12.50±5.61% to 9.62±3.52%, P = 0.039; cryopreserved PBMCs: from 22.7±6.1% to 19.1±7.0%, P = 0.012). In contrast, the decrease in H2O2-induced DNA damage observed in the cryopreserved cells masked the protective effect of the wild blueberry drink documented in the fresh samples (fresh PBMCs: from 44.73±7.46% to 36.34±9.27%, P < 0.001; cryopreserved PBMCs: from 25.8±4.6% to 23.9±4.6%, P = 0.414). In conclusion, our results suggest that FPG-sensitive sites, and more importantly, H2O2-induced DNA damage could be significantly modified following the long-term storage of samples obtained from individuals participating in a dietary intervention study. Because storage may affect the assessment of the protective role of diet against DNA damage as a marker of oxidative stress, further research is needed.