Patients with peach allergy who experience severe symptoms, including anaphylaxis, reportedly have a higher positivity for peach gibberellin-regulated protein (GRP)-specific immunoglobulin (Ig) E than those with only oral symptoms. However, a study in Italy investigating apple allergy (another Rosaceae fruit) found no clear association between apple GRP-specific IgE levels and clinical disease types. This study aimed to evaluate the clinical utility of GRP-specific IgE measurement in Japanese patients with apple allergy. We collected sera from apple-allergic patients in Japan and measured their IgE levels specific to apple GRP. Apple-allergic patients (14 with oral reactions and 14 with systemic reactions) and seven non-allergic controls were examined. The specific IgE levels against apple, Mal d 1, Mal d 4, Japanese cedar, Japanese alder, Japanese white birch, Bet v 1, and Bet v 2 were also determined using 3gAllergy™. Positive results for apple-GRP-specific IgE by enzyme-linked immunosorbent assay were obtained in one patient with oral reactions and in seven cases of systemic reactions. Exercise as a cofactor was involved in cases with high apple GRP-specific IgE. GRP expression was considerably lower in apples than in peaches, as detected by reverse transcription-quantitative polymerase chain reaction testing. Thus, GRP-specific IgE may be an important marker for diagnosing systemic reactions triggered by exercise in fruits with low GRP expression, such as apples.