Objective:To study the effects of periodontal scaling on microorganism in periodontal pocket and gingival crevicular fluid in patients with periodontitis.Methods:60 cases of periodontitis were selected and divided into 2 groups randomly with 30 in each group.The patients in scaling group were treated by periodontal scaling, those in control group by gargle with chlohexidine.Before and after treatment the microorganism in pocket bottom of each patient was measured by Congo red negative dyeing.Gingival index(GI), probing depth(PD) and gingival crevicular fluid(GCF) were also measured, the relationship between periodontal scaling and clinical indices was analysed.Results:In scaling group the percentage of coccoid cells in pocket bottom increased more after scaling,that of bacillus,spirochetes decreased, PD,GCF value were all decreased (P0.05).Conclusion:Periodontal scaling can decrease the percentage of pathogenesis bacteria in periodontal pocket bottom and decrease PD,GI and GCF values.