This longitudinal study evaluated the response to periodontal treatment by subjects infected with either JP2 (n ؍ 25) or non-JP2 (n ؍ 25) Aggregatibacter (Actinobacillus) actinomycetemcomitans. Participants were treated during the first 4 months by receiving (i) scaling and root planing, (ii) systemic antibiotic therapy, and (iii) periodontal surgery. Probing depth (PD), clinical attachment level (CAL), and gingival and plaque indices (GI and PI, respectively) were monitored at baseline and at 12 months, along with DNA-PCR-based subgingival detection of JP2 or non-JP2 A. actinomycetemcomitans. At baseline, PD, CAL, and GI scores were statistically higher in the JP2 strain-positive group than the non-JP2-strain-positive group. At 12 months, PD, CAL, and GI scores had decreased significantly for both groups, but the reduction rates of PD and CAL were higher in the non-JP2-strain-positive group. Among JP2-strain-positive patients in the baseline, patients who remained JP2 strain positive at 12 months showed significantly higher GIs than did the patients who had lost the detectable JP2 clone. Patients who remained JP2 strain positive at 12 months appeared to be more resistant to mechanical-chemical therapy than did those who were still non-JP2 strain positive, while the elimination of JP2 A. actinomycetemcomitans remarkably diminished gingival inflammation. Early identification and elimination of the JP2 clone of A. actinomycetemcomitans will enable practitioners to effectively predict the outcome of treatments applied to periodontal patients.Compared to gingivitis, or disease-free periodontium, an increased incidence of Aggregatibacter (Actinobacillus) actinomycetemcomitans has been reported in the lesions of localized aggressive periodontitis (LAP) or severe chronic periodontitis (9,13,16,41,44,45). It is also true that while polymicrobial infection is implicated in the pathogenesis of chronic adult periodontitis, oral colonization by A. actinomycetemcomitans is more directly associated with the pathogenesis of LAP. Such pathogenic outcomes related to A. actinomycetemcomitans infection seem to be partially derived from leukotoxin (LTX) produced by A. actinomycetemcomitans. LTX is a potent virulence factor, which is encoded in an operon consisting of four genes (5) and typically causes cytotoxicity in neutrophils (26) and macrophages (37). Furthermore, in vitro experiments revealed that a specific 530-bp sequence in the LTX promoter region, rather than the LTX operon, impacts the transcription regulation of LTX (5), whereas there are several factors that regulate the expression of LTX from A. actinomycetemcomitans (25). It is also true that there may be highly leukotoxic A. actinomycetemcomitans strains other than just the type with the 530-bp deletion (24). Nonetheless, the deletion of this 530-bp promoter region, which is found in some pathogenic strains of A. actinomycetemcomitans, also called JP2 strains, has critical ramifications. For example, faster expression of the LTX gene with the deletion has been o...