This research was undertaken to determine the population of a high-virulence strain of Salmonella enterica serovar Enteritidis in partridge by a fluorescent quencher PCR assay and to correlate these findings with the results obtained from the immunohistochemical localization and histopathological examinations of selected Salmonella enterica serovar Enteritidis-infected tissues. To make the results meaningful, a side-by-side bacteriology method (indirect immuno-fluorescent antibody staining) was performed too. The results of indirect immuno-fluorescent antibody staining and immunohistochemical localization were similar to the fluorescent quencher PCR assay. The time course of the appearance of bacterial antigens and tissue lesions in various tissues was coincident with the levels of the bacterial DNA loads at the infection sites. This suggests that Salmonella enterica serovar Enteritidis loads in internal organs are closely correlated with the progression of the infection.