This study aimed to evaluate tryptase and E-cadherin protein expression in odontogenic keratocysts (OKCs) and radicular cysts (RCs) and their relationship with lesion size. Thirty OKC and 30 RC cases were analyzed by immunohistochemistry. Tryptase expression was quantitatively assessed using the quantification of mast cells, and expression of E-cadherin was semi-quantitatively analyzed estimating the proportion of positive cells: 1 = less than 25% of immunopositive cells; 2 = 26 to 50% of immunopositive cells; 3 = 51 to 75% of immunopositive cells; 4 = more than 75% of immunopositive cells. Data on cystic lesion sizes were obtained from patients' clinical files, based on previous radiographic exams, and the lesions were categorized into three groups: group 1 (< 2 to 2cm); group 2 (> 2 to 4cm), and group 3 (> 4cm). Higher mast cell means were found for RCs, with the predominance of degranulated mast cells in both OKCs and RCs (p = 0.082). Concerning the epithelial component, a higher concentration of degranulated mast cells was detected in RCs (p = 0.000). Regarding connective tissue, degranulated mast cells were more evident in OKCs (p = 0.762). A negative correlation was observed between E-cadherin expression and total number of mast cells (p = 0.011), degranulated mast cells (p = 0.040), and degranulated mast cells in both superficial (p = 0.035) and deep connective tissues (p = 0.009). Concerning lesion size, a negative correlation with total number of mast cells (p = 0.016) and number of degranulated mast cells (p = 0.049) was observed, both in the epithelial components. Herein, the larger the lesion size, the lower the number of degranulated mast cells in the epithelium (r = - 0.271; p = 0.49), suggesting that these cells play a role in the initial cystic expansion phase. The higher expression of tryptase in degranulated mast cells was linked to a lower expression of E-cadherin, which may be related to a change in the epithelial permeability in these lesions, contributing to increased cystic content and lesion growth. Evidence of the relationship between mast cells and E-cadherin in the growth of odontogenic cysts was studied.