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Heating is the most common egg pasteurization technology to minimize the risk of Salmonella Enteritidis. We hypothesize that slow heating rate (SHR) during come-up stage, as practiced commercially, could trigger heat stress response in Salmonella that compromises product safety. The expression level of Salmonella heat-stress-response genes (htrA, clpB, and grpE) and virulence genes (hilC, sipA, and pipB) at different heating rate during come-up stage were measured by RT-qPCR. SHR caused more profound expression (> +2-fold change) of heat resistant genes than fast heating rate (FHR). The expression of virulence varied by genes. To understand how different heating rates during come-up stage could affect the heat resistance of Salmonella during the holding stage, D53℃ and D55℃ were measured by plate-counting on TSA and XLT-4. D53°C from FHR was significantly shorter than that from D53°C of SHR (8.9±1.6 vs. 14.4±1.3min by TSA; 6.7±1.9 vs. 12.0±1.6min by XLT-4). D55℃ resulted from two heating rates did not differ significantly. Bacterial population in yolk was monitored by plate-counting on TSA and XLT-4 to determine the recovery of Salmonella from the heat injury during the 8-h cooling. During the first 30min of cooling, Salmonella population with FHR decreased by additional 1.3±0.5 log whereas no reduction was observed with SHR. The overall recovery of Salmonella from SHR and FHR on TSA was 1.6±0.4 CFU/ml and 0.7±0.5 CFU/ml, respectively, and on XLT-4, 2.9±0.2 CFU/ml and 1.7±0.3 CFU/ml, respectively. Our study indicated FHR at come-up stage could result in safer pasteurized shell eggs, compared to SHR.