Objective: To explore peptidomic changes of peptides in saliva and gingival crevicular fluid (GCF) before and after treatment of gingivitis. Methods: From January 2017 to September 2017, seventeen participants at the age of 24-62 (6 males and 11 females) at Department of Preventive Dentistry, Peking University School and Hospital of Stomatology with gingivitis were recruited in the present study. Their clinical parameters were measured and recorded. Saliva and GCF samples were collected from each of the participants at the baseline and 7 days after ultrasonic supragingival scaling, respectively. Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) was employed to detect the changes of peptidomic profiles, while ano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC/ESI-MS/MS) was performed to identify the possible proteins from which the peptides might derive. Results: Initially, four peptide peaks [mass-to-charge ratio (m/z) values: 1 030.6, 1 043.4, 1 053.4 and 1 064.6] were screened out exhibiting a decreasing trend after treatment (P<0.05). Besides, five peptide peaks from gingival crevicular fluid (P<0.05) exhibited differential expression, among which 1 055.5 and 1 168.3 demonstrating a decrease after treatment, while 3 363.7, 3 480.9 and 3 489.5 increased overtime. Certain positive correlations were detected between some peptides and clinical parameters. Principle component analysis using the above mentioned peptide peaks showed a distinct distribution before and after treatment and peptides from GCF showed a slightly better capacity to discriminate patients before and after treatment. The peptides with m/z values of 1 055.5 in GCF and 1 064.6 in saliva were identified to be segments of serum albumin and complement C3, respectively. Conclusions Several differentially expressed peptides were detected in saliva and GCF by MALDI-TOF MS, exhibiting the potentiality to act as biomarkers in gingivitis patients.