The aim of the present study was to determine sequence variation in the Lys-x-specific protease (Kgp) encoding gene kgp of Porphyromonas gingivalis and to analyze its association with periodontal disease severity. Pooled subgingival plaque samples were obtained from the six most severely affected sites of 102 patients with periodontitis. Sequence analysis of the kgp gene in 23 clinical P. gingivalis isolates resulted in the identification of two distinct kgp types (kgp-I and kgp-II) according to sequence differences in the region encoding the catalytic domain. Restriction analysis revealed that 59 of the 102 patients were colonized by kgp-I and 43 by kgp-II. Patients harboring kgp-I or kgp-II showed no significant difference in the severity of periodontal disease as assessed by pocket probing depth and bleeding on probing following adjustment for smoking habit and age. Moreover, no differences in proteolytic activity of Kgp-I and Kgp-II were detected. The results indicated that two kgp types are maintained in natural populations of P. gingivalis.