Objective To investigate 7 short chain fatty acids (SCFA) concentrations in gingival crevicular fluid(GCF) of aggressive periodontitis(AgP) and to analyze the relationship between levels of SCFA and AgP clinical parameters. Methods GCF was collected from 152 sites of 38 AgP patients and 56 sites of 14 healthy subjects. Formic acid, succinic acid, acetic acid, lactic acid, propionic acid, butyric acid and isovalerianic acid were detected by high performance capillary ehctrophoresis. Results The concentrations of succiaic acid, acetic acid, lactic acid, propionic acid, butyric acid and isovalerianic acid in GCF were significantly higher in AgP patients than in healthy group, while formic acid was lower in GCF of AgP group compared with healthy group. Correlation analysis showed that formic acid was negtively correlated with bleeding index(BI), probing depth(PD) and attachment loss(AL), while BI was positively correlated with sueeinie acid, acetic acid, lactic acid,propionic acid and butyric acid; PD and AL were positively correlated with succiaic acid, acetic acid, propionic acid, butyric acid and isovalerianic acid. Conclusions The elevation of succinic acid, acetic acid, propionic acid, butyric acid and isovalerianic acid concentrations in GCF may be related with AgP destruction condition, while formic acid concentration was reduced.