In this study, the nucleotide sequences of the prtC genes of six clinical Porphyromonas gingivalis isolates obtained from patients with periodontitis and from reference strain 53977 were determined. All analyzed genes were heterogeneous in their nucleotide composition and differed in up to 13 nucleotides. Moreover, substantial differences were found in comparison to prtC of reference strain 53977. The prtC genes of 45 Porphyromonas gingivalis isolates were amplified by polymerase chain reaction (PCR) and the PCR products were also digested with restriction endonucleases Tsp509I, NlaIII and DraII (PCR-restriction fragment-length polymorphism). Nine different restriction pattern combinations were observed, with four being most frequent (28.9%, 26.7%, 17.8% and 11.1%). The data presented here demonstrates that prtC genes are heterogeneous in their nucleotide sequence and therefore may be used as a target for molecular epidemiological studies. The observed heterogeneity of prtC genes may be a result of microevolution processes.