To determine the prevalence of Salmonella serotype Enteritidis in eggs in South Korea, we conducted a microbiological survey of commercially available eggs produced in conventional or organic farms during the period from 2010 to 2012. The contents of 7,000 raw shell eggs (6,000 of conventional and 1,000 of organic origin) were examined to evaluate the extent and type of Salmonella Enteritidis contamination. A total of 26 salmonellae (7.4% of all pooled samples) were isolated from 350 homogenized pools, each containing the contents from 20 eggs. An unexpected and particularly surprising finding was that all the Salmonella isolates were serotyped as Salmonella Gallinarum. Salmonella Gallinarum was more common in eggs from organic farms: 10 of 50 egg pools (20.0%) from organic and 16 of 300 egg pools (5.3%) from conventional farms tested positive for Salmonella Gallinarum. However, organic and conventional isolates showed similar antimicrobial susceptibilities. All the isolates and a vaccine strain, SG 9R, which has been widely used in South Korea, were further characterized using the automated repetitive sequence-based PCR (rep-PCR) system, DiversiLab, to ascertain the molecular subtypes and to identify differences from the vaccine strain. The rep-PCR identified 2 distinct clusters among the 26 Salmonella Gallinarum isolates with a greater than 96% similarity index. These were clearly differentiated from the vaccine strain, SG 9R, with which there was a less than 86% similarity index. We found there was low genetic heterogeneity among isolates within each cluster and were able to distinguish wild type strains from the live vaccine strain (SG 9R) using the DiversiLab system.