The aim of this study is to determine whether either gingival crevicular fluid (GCF) bacterial gingivain/gingipain or dipeptidyl peptidase (DPP) levels, total activity (TA) and concentration (EC), predict progressive attachment loss (AL) in 75 patients with moderate periodontitis. GCF was collected from 16 molar and premolar mesiobuccal sites and then clinical attachment level (CAL) and probing depth (PD) were measured with an electronic constant pressure probe. Lastly, gingival, gingival bleeding, and plaque indices were scored. Prior to the baseline visit, patients were given basic periodontal treatment after which the above procedures were repeated. In addition, carefully localized radiographs were taken of the test teeth and repeated annually. Patients were then seen every 3 months for 2 years and the clinical measurements repeated at each visit. In 48 patients, 124 AL sites, 91 rapid AL (RAL), and 33 gradual AL (GAL) were detected. Gingivain/gingipain and bacterial DPP levels (TA and EC) at RAL sites were significantly higher (P < or = 0.0001) than at paired control sites at the attachment loss time (ALT) and prediction time (PT). Mean levels over the study period of both proteases (TA and EC) at GAL sites were significantly higher (P < or = 0.0001) than those at paired control sites. The GCF levels of gingivain/gingipain were always higher than those of DPP. Critical values (CV) of 5 microU/30 seconds (TA) and 30 microU/microL (EC) for both proteases showed high sensitivity and specificity values for TA and EC, which were the same at both ALT and PT. The positive predictive values were higher for gingivain/ gingipain. Mean site levels, over the course of the study, of both proteases (TA and EC) were significantly higher (P < or = 0.0001) at AL, RAL, and GAL sites than non-attachment loss (NAL) sites in AL patients and mean patient levels were significantly higher (P < or = 0.0001) in AL, RAL, and GAL patients than NAL patients. These results indicate that both of these bacterial proteases in GCF may be predictors of periodontal attachment loss.