We investigated stable organic radicals formed in response to cold stratification in ‘Fuji’ apple seeds using X-band (9 GHz) electron paramagnetic resonance (EPR) technique. This technique primarily detected two paramagnetic species in each seed. These two different radical species were assigned as a stable organic radical and Mn²⁺ species based on the g values and hyperfine components. Signal from the stable radicals was noted at a g value of about 2.00 and was strong and relatively stable. Significant radical intensity changes were observed in apple seeds on refrigeration along with water supplementation. The strongest radical intensity and a very weak Mn²⁺ signal were also observed for the seeds kept in moisture-containing sand in a refrigerator. Noninvasive EPR of the radicals present in each seed revealed that the stable radicals were located primarily in the seed coat. These results indicate that the significant radical intensity changes in apple seeds under refrigeration for at least 90 days followed by water supplementation for one week, can be related to cold stratification of the seeds.