The purpose of the present study was to investigate the bacterial communities associated with asymptomatic and symptomatic endodontic infections and to compare denaturing gradient gel electrophoresis (DGGE) fingerprinting patterns of these two clinical conditions. The root canal microbiota of teeth associated with asymptomatic or symptomatic periradicular lesions was profiled by the PCR-DGGE method and then compared, taking into consideration the banding patterns. Bacteria were present in all examined cases. Comparative analysis of the two clinical conditions revealed bands that were common to both symptomatic and asymptomatic cases, but most DGGE bands appeared to be unique for each clinical condition. No single band occurred in all profiles. The mean number of bands detected in the 16S rDNA community profiles were 12.1 ± 9.4 (range 2-29) for symptomatic samples and 6.7 ± 2.7 (range 2-11) for asymptomatic ones. Clustering methods and principal component analysis of DGGE banding pattern placed the samples according to the presence or absence of symptoms. Four intense bands that were excised from the gel and sequenced showed similarities to species of the Campylobacter genus (found in 5/12 asymptomatic and in 3/11 symptomatic cases), Fusobacterium genus (4/11 symptomatic cases), Acinetobacter genus (5/12 asymptomatic cases), and Enterobacteriaceae family (11/12 asymptomatic and 2/11 symptomatic cases). The profiles of the predominant bacterial community appeared to be unique for each individual. These findings confirm that endodontic infections are polymicrobial and showed that there are significant differences in the predominant bacterial composition between asymptomatic and symptomatic cases.