Background The search of criteria of differential enzymatic activity of cyclooxygenase-2 and matrix metalloproteinases immunocompetent cells of granulomas in the primary and secondary apical periodontitis (AP) provides information about the features of lesions of periodontal stromal component, and it can be used as the basis for future therapeutic intervention. Objective. The purpose of this study was to compare the qualitative and quantitative characteristics of the cellular composition of granulation tissue, which formed during primary and secondary apical periodontitis; comparison of morphological characteristics of the structure apical granuloma with immunohistochemical indicators of markers expression of cluster of differentiation CD3, CD4, CD8, CD68, CD138, CD20 and cyclooxygenase-2 and matrix metalloproteinase 9. Methods. The study included 59 patients aged 18 to 50 years with apical periodontitis. Patients were divided into 2 clinical group: 1 – with primary periodontitis and 2 – with secondary periodontitis. For morphological studies using peryapikalnoyi granulation tissue biopsies. Results. Significant differences were found for the fractions of CD4+ T helper cells (p=0,034, r=0,321), CD20+ mature B lymphocytes (p=0,001, r=0,671), CD68+ macrophages (p=0,011, r=0,684) and CD138+ plasma cells (p=0,002, r=0,645). And, also likely decrease in the ratio of CD4+/CD8+ (p=0,002, r=0,645), by reducing the fraction of CD4+ T-helper cells, against reducing the number of leukocytes, expression of MMP-9 (p=0,04, r=0,302) and COX-2 (p=0,013, r=0,321) with secondary apical periodontitis, compared to the primary periodontitis. Conclusion. Disease progression and the beginning of the destruction of bone tissue with the formation of granulation tissue is the result of abnormal immune responses, III and IV type hypersensitivity reactions, with the formation of immune granulomas.