Cystatins are physiological inhibitors of cysteine proteinases and widely distributed in human tissues and fluids including saliva. Cystatins S, SA, SN, and D are only found in glandular saliva and tear fluid whereas cystatin C has been detected in all tested biological fluids. Previous studies demonstrated that total cystatin activity and cystatin C concentration were highest in whole and parotid saliva of periodontitis patients compared to healthy subjects suggesting a response of the salivary glands to an inflammatory condition of the oral cavity. Based on these results we studied a possible change in the concentration of cystatin S, cystatin C, albumin, IgA, amylase activity, and cystatin activity in a whole and parotid saliva of 20 periodontitis patients as a consequence of periodontal treatment. Saliva samples were quantified for cystatins S and C, albumin, and IgA by enzyme-linked immunosorbent assay. Amylase was determined in an activity assay and total cystatin activity was measured towards pa-pain. The clinical condition of the subjects improved significantly after 6 months of periodontal therapy whereas biochemical analyses of whole and parotid saliva indicated that significant changes in salivary protein composition occurred only in whole saliva. Total cystatin activity (P < 0.05) and cystatin C concentration (P < 0.05) of whole saliva samples collected after periodontal treatment decreased to normal healthy control values. Further, concentrations of cystatin S were unchanged during the periodontal treatment process. These results suggest that other sources of cystatins than the parotid gland i.e.; other salivary glands or crevicular fluid, are involved in the decrease of total cystatin activity in whole saliva after periodontal treatment.