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Collections of deletion mutants are important tools for functional genomics in crops. In order to establish an efficient physical γ-ray-based mutagenesis protocol and estimate the frequency of induced chromosome deletion events in apple, we mutagenized a total of 338 leaves of the apple cultivar ‘Golden Delicious’ with a range of irradiation doses (from 0 to 30 Gy). After in vitro culture and regeneration, a total of 248 plantlets were genotyped by a custom-made 384 SNP-based array suited to identify homozygous regions, corresponding to chromosome deletions produced by the irradiation and/or the in vitro culture treatments. With this approach, we identified nine multi-SNP chromosome deletions corresponding to 3.7 % of all regenerated plantlets and ranging from one to 44 cM (0.1–20.2 Mb). Chromosome deletions were also observed at mildly, not significantly lower frequency in plantlets regenerated from non-irradiated leaves. Our results confirm the possibility to generate apple plants with sizeable deletions of known dimension and location, opening the way to creating a collection of deletions spanning the apple genome useful for functional genomics. The high frequency of deletions apparently caused by somaclonal variation deserves further investigation.