Objective: Microbiota in the upper respiratory tract begins to form immediately after birth. Aerobic and anaerobic flora will form when a healthy child reaches the age of five. Tonsillitis and adenoiditis are the most common upper respiratory tract infectious diseases in childhood and adulthood. Transmission of bacterial infections from tonsils to adenoid tissue (endogenous transmission) can be prevented by usage of suitable antibiotics. At the same time, continuous exogenous infections of each or both sites require adenotonsillectomy surgery. In this study, to understand the role of endogenous transmission of Haemophilus influenzae (H. influenzae) in adenotonsillectomy, we aimed to investigate the genetic relatedness of H. influenzae strains obtained from the tonsil and adenoid of the same patient. Materials and Methods: Twenty eight patients were included the study for displaying the growth of 56 H. influenzae strains (28 isolates per site). We investigated the genetic relatedness of H. influenzae strains obtained from the tonsils and adenoids of the patients by using the pulsed-field gel electrophoresis (PFGE) method. Results: Twenty one isolates were isolated from the tonsils and adenoids of unrelated patients. We excluded nine (32.2%) out of 28 patients’ H. influenzae isolates from the study, that had identical strains depending on the ≥80% similarity Dice coefficient. Conclusion: The probability of endogenous transmission between the two sites was very high, which means that some adenotonsillectomy surgery might be avoided and treated with antibiotics.