A total of 191 samples collected from the commercial swine farms located in Chungnam province were investigated by PCR to estimate the prevalence of Lawsonia (L.) intracellularis infection. In the group of the pigs with proliferative enteritis, 14 (93.3%) of 15 intestinal samples and 12 (80.0%) of 15 feces were positive in PCR. In contrast, a relatively low positive rate (18.0%, 29 of 161 samples) was determined in the group of normal healthy pigs. The group of pigs over 120 days showed the highest positive rates (26.8%, 15 of 56 samples). In the comparison of the sequences of 210bp for species specific fragments and 301bp for outer membrane protein, the isolates (L1. L2) showed almost 100% identity with the reference L. intracellularis (L08049, USA). For the sequences of partial 16s rDNA, the homologies among the 5 isolates (L1-L5) were 97.4% to 99.3%, and those of 5 sequences (L1-L5) versus 5 overseas reference strains of L. intracellularis ranged from 98.6% to 99.8%. In the comparison of the nucleotide sequences among 5 isolates and other species in Desulfovibrionales showed 82.4 to 99.5% identities. The 5 isolates shared relatively low identities (76.9% to 84.4%) with the species of alpha-proteobacteria. In phylogenetic analysis based on the 16s rDNA sequences, all of the 5 isolates (L1-L5) were located in the same branch with the strains of L. intracellularis that were previously isolated from the pigs in USA and China. Seven strains of Desulfovibrio sp. were clustered in the neighboring branches, whereas alpha and gamma Proteobacteria showed distant relationship with L. intracellularis strains. The present findings suggest that L. intracellularis infection is endemic in the swine farms in the regions, and that the domestic isolates maintained very limited genetic variation.