So far, it was not possible to establish whether spores of Bacillus isolates could survive high heat treatments (i.e., at least 30 min 100°C) unless their survival was assessed in an experimental setting. We recently identified a mobile genetic element that is responsible for high level heat resistance of Bacillus subtilis spores. It encodes proteins that are specifically expressed during spore formation. The presence of this element in the genomes of wide array of Bacillus species was investigated and could be linked directly with high-level heat resistance of spores of certain B. subtilis strains. Moreover, this was also demonstrated for high-level heat resistance of spores of certain B. amyloliquefaciens and B. licheniformis strains. In addition, we established that the copy number of the element correlated positively with further increased heat resistance of spores. The presence or absence of this element can now be established by PCR, and based on the established heat inactivation kinetics of the spores of a large range of individual strains, optimal heat treatments can be designed to inactivate such spores in foods.