Objectives: Periapical inflammation is one of the most common pathologies within the jaws, leading to the destruction of periodontal ligaments, bone resorption and the formation of periapical granulomas or radicular cysts. The final diagnosis can be made only on the basis of histopathological examination. The aim of the study was to assess the conformity between clinical and histopathological diagnosis of inflammatory periapical lesions treated with apicoectomy. Materials and Methods: The case histories of 52 patients subjected to surgical treatment at the Clinic of Conservative Dentistry with Endodontics between 2008 and 2018 were analyzed. Demographic data (age, gender), clinical (radiological) diagnosis, and data on the presence of sinus tracts and causal tooth were obtained from patients’ records. Results: In the light of clinical and radiological examination, 32 (61.5%) periapical granulomas, 18 (34.6%) radicular cysts and 2 (3.9%) periapical scars were diagnosed, whereas the result of histopathological examination revealed granuloma in 34 (65.4%) cases and in 18 (34.6%) - radicular cyst. For clinical diagnosis of granuloma, the result coincided with the result of the histopathological examination in 28 cases, and in the case of cysts in 14. The analysis showed a significant relationship between the clinical and histopathological diagnoses (p <0.05). Conclusions: The study emphasizes the importance of histopathological assessment for the proper diagnosis of periapical lesions. Clinical Relevance: The article emphasizes the high importance of histopathological examination for the correct diagnosis of chronic inflammatory periapical lesions.