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To assess the contribution of ozone to lethality of Salmonella enterica serovar Enteritidis in experimentally inoculated whole shell eggs that are sequentially treated with heat and gaseous ozone in pilot-scale equipment.Whole shell eggs were inoculated with small populations of Salmonella Enteritidis (8·5 × 104–2·4 × 105 CFU per egg) near the egg vitelline membrane. Eggs were subjected to immersion heating (57°C for 21 min), ozone treatment (vacuum at 67·5 kPa, followed by ozonation at a maximum concentration of approx. 140 g ozone m−3 and 184–198 kPa for 40 min) or a combination of both treatments. Survivors were detected after an enrichment process or enumerated using modified most probable number technique. Ozone, heat and combination treatments inactivated 0·11, 3·1 and 4·2 log Salmonella Enteritidis per egg, respectively.Sequential application of heat and gaseous ozone was significantly more effective than either heat or ozone alone. The demonstrated synergy between these treatment steps should produce safer shell eggs than the heat treatment alone.Shell eggs are the most common vehicle for human infection by Salmonella Enteritidis. Many cases of egg-related salmonellosis are reported annually despite efforts to reduce contamination, including thermal pasteurization of shell eggs and egg products. Treatment with ozone-based combination should produce shell eggs safer than those treated with heat alone.