Background and Objective: Aggressive periodontitis is a destructive disease that leads to a quick and extensive periodontal tissue loss. Mast cells are known to play important roles in allergic reactions, host defense against bacterial infections, local homeostasis, inflammation, and angiogenesis. The aim of the present study was to evaluate the relationship between mast cell numbers and aggressive periodontitis. Materials and Methods: A descriptive analytical and blind study was designed and gingival specimens from 19 moderate to advanced aggressive periodontitis sites (case group) and 18 gingivitis sites (control group) was taken during flap and crown lengthening surgeries. Toluidine blue and Hematoxylin Eosin staining were done for mast cell counting and inflammation assessment, respectively. Inflammatory and mast cells in 5 micron sections were assessed by two trained observers utilizing light microscopy. ANOVAs and T test with an alpha error level less than 5% were used to analyze the data. Results: The mean values of the mast cell numbers were 7.6 10.8 and 9.8 13.0 in aggressive periodontitis and gingivitis sites, respectively. There were no statistically significant differences among the mast cell counts, clinical attachment loss, or pathologic inflammation (P> 0.05). Conclusions: The present study indicates that mast cell numbers were not significantly different between aggressive periodontitis and gingivitis. Further studies are required to evaluate dynamic aspects of host defense.