Early infection may result in long-term colonization of layers with Salmonella enterica sv. enteritidis (S. enteritidis, SE), resulting in shedding into table or hatching eggs. To evaluate genetic factors underlying early response to SE, genetic line differences in mortality and pathogen load at two sites (cecal lumen and spleen) were investigated. At day of hatch, chicks of four genetic lines were intra-esophageally inoculated with one of three doses of SE phage type 13a. There was a significant effect (P < 0.001) of genetic line on chick 6-d survival. The effect of genetic line was significant (P < 0.05) on survivors’ SE burden in cecal content but not on SE burden per gram of spleen. The SE pathogen load of the spleen and the cecal content were not significantly correlated, indicating that independent host mechanisms are partly responsible for these two traits. Genetic line differences in chick survival and SE colonization of cecal content were demonstrated in young layer chicks.