Resistance of Campylobacter jejuni to environmental stress is regarded as a risk factor for the transmission of C. jejuni from poultry or poultry products to humans. So far, the mechanisms underlying the capacity of C. jejuni to survive environmental stress conditions are not fully understood. In this study, we searched for polymorphisms in C. jejuni genes, potentially involved in resistance to chill stress. To this end, we assessed 3 groups of C. jejuni isolates (clinical, retail chicken meat, and feces) for survival of experimentally induced chill stress. For each isolate we sequenced 3 genes encoding the C. jejuni sigma factors FliA, RpoD, and RpoN as well as the genes for the transcriptional regulator SpoT and the periplasmic protein HtrA. Data suggest a higher prevalence of a specific polymorphism in spoT in clinical isolates compared with poultry meat or farm isolates. Moreover, this genotype correlated with enhanced survival of chill stress. The observation that the prevalence of this SNP is relatively high in clinical isolates, which most likely have been exposed to multiple forms of stress, suggest that this SNP may be a biomarker for enhanced survival of stress.