The flora of the periodontal pocket in periodontal disease is highly complex. Investigation of the disease-associated changes in flora is difficult and is subject to many uncertainties. Development of molecular biological methods for use in microbial identification has enabled a re-evaluation of the complex flora associated with periodontal disease. Objectives: The aim of this preliminary study was to use culture-independent methods to estimate bacterial diversity in Icelandic subjects. Methods: Samples were collected, from three subjects with chronic adult periodontal disease, by inserting paper points into several periodontal pockets and with a periodontal scaler to scrape one deep pocket. The 16S rRNA genes of the microbial flora in the clinical samples were amplified directly by PCR with bacterial universal primers. PCR products were cloned and sequenced. Results: A total of 373 clones were sequenced, analysed and 62 different species or phylotypes identified from 7 bacterial phyla. Most of the species found are known to be cultivable but several uncultivable phylotypes were found in all three patients; two phylotypes were identified from the newly described TM7 phyla. Most diverse group of species fell into the phylum firmicutes including predominant species as Streptococus constellatus, S. intermedius, Selenomonas sputigena and Peptostreptococcus micros. Putative pathogens such as Fusobaterium nucleatum, Atopobium sp. and Actinomyces sp. were also detected. However, pathogens known to be associated with periodontal disease such as Prevotella sp., Porphorymonas gingivalis and Actinobacillus actinomycetemcomitans were not identified in these samples. Conclusions: In complex microbial communities such as the oral cavity, culture-independent approaches are useful and might reveal undiscovered pathogens. These methods give clues to the composition of the bacterial flora and can be used as a tool to find new putative pathogens associated with the disease. Failure to find the classical cultivable pathogens in these samples should prompt further study.