OBJECTIVES: The study aimed to test the presence of pepsin in saliva samples of subjects by electrophoresis, and in samples of palatine tonsils by immunohistochemical staining. Furthermore, the study focues on examining the association between the presence of pepsin and the expression profile of AID and APOBEC3 in the lympathic tissue of the palatine tonsils. Finally, the objective of this study was to test the expression of AID and APOBEC3 in the lymphatic tissue of the palatine tonsils using the RT – PCR method. STUDY DESIGN: The research was structured as original cross – sectional study. PARTICIPANTS AND METHODS: There were 80 patients under the age of 18 with a previously established indication for tonsillectomy who were included in the study. Participants were divided into two groups based on Western blot analysis of pepsin in the saliva sample taken before surgery. Samples of removed palatine tonsils were subjected to immunohistochemical staining to confirm the presence of pepsin, and then the expression of AID, A3B and A3G genes in the samples were measured using the RT – PCR method. RESULTS: No significant differences were observed in the expression of AID, A3B and A3G genes with regard to the immunohistochemical findingof pepsin in the palatine tonsils. There is significant, positive and weaker relationship between patient age and A3G gene expression in palatine tonsil samples. With higher expression of A3B gene, the expression of the AID gene in palatine tonsil samples is also higher. A higher expression of the A3G gene implies a higher expression of the A3B gene in palatine tonsil samples. No significant differences in gene expression were observed with respect to gender. CONCLUSION: This research confirmed the presence of pepsin in more than half of the subjects' saliva and palatine tonsil samples. There was no significatnt influence of pepsin on the expression of AID and APOBEC3 components and the hypertrophy of the lymphatic tissue of palatine tonsils in the investigated pediatric population.