The objective of this study was to understand the distribution patterns and levels of Salmonella Enteritidis (SE) in the immune organs of ducklings after oral challenge. We conducted serovar-specific real-time polymerase chain reaction (PCR) for SE to detect the genomic DNA of SE in the blood and immune organs, including the bursa of Fabricius, thymus, spleen, and Harderian gland, from ducklings after oral challenge at different time points. The results showed that SE was consistently detected in all the samples. The Harderian gland and spleen tested positive at 8 hr postinoculation (PI). The organism was detected in the blood, bursa of Fabricius, and thymus at 10 hr PI. The copy number of SE DNA in each tissue reached a peak at 24-36 hr PI. The spleen, blood, and Harderian gland contained high concentrations of SE, whereas the thymus and bursa of Fabricius had low concentrations. SE populations began to decrease and were not detectable at 2 days PI, but they were still present up to 9 days PI in the spleen, without producing any apparent symptoms. To validate these results, the indirect immunofluorescent antibody (IFA) technique was used, and the IFA results were similar to those of the fluorescent quantitative-PCR. In conclusion, the results provided insight into the SE life cycle in the immune organs; furthermore, the Harderian gland and spleen were determined to be the primary sites of invasion among the immune organs of normal ducklings after oral SE challenge. This study will help in understanding the pathogenesis of SE infection in vivo and may help in the development of a live Salmonella vaccine in the future.