Seeds stored in controlled conditions in gene banks, faster or slower lose their viability. The effects of seed moisture content levels (ca. 5, 8, 11%) combined with storage temperatures (-3˚,-18˚,-196˚C) were investigated in terms of the description of seeds defined as orthodox under oxidative stress after seed storage, during germination, and initial seedling growth. Hydrogen peroxide (H 2 O 2), thiobarbituric acid reactive substances (TBARS) and ascorbate (Asc) were analyzed in relation to seed germinability and seedlings emergence in three species: Malus sylvestris L., Prunus avium L. and Prunus padus L. The effect of seed storage conditions on H 2 O 2 levels appeared in germinated seeds after the third year of storage in each species. The H 2 O 2 levels were negatively correlated with the germination and seedling emergence of P. avium seeds after three years of storage under all examined combinations. The emergence of P. padus seedlings was not linked to any of the stress markers tested. The P. padus seed biochemical traits were least altered by storage conditions, and the seeds produced tolerant seedlings of relatively high levels of H 2 O 2 and TBARS. To cope with different H 2 O 2 levels, TBARS levels, and Asc levels in seeds of three species varying storage conditions different molecular responses, i.e. repairing mechanisms, were applied during stratification to compensate for the storage conditions and, as a result, seeds remained viable and seedlings were successfully established.