Background: Adenoid and tonsils which play a protective role against infections in healthy individuals may become a reservoir for pathogenic microorganisms. Infection of the adenoid and palatine tonsils continue to be a major burden among children in our environment. Bacteria colonize the surface and core of the adenoid and tonsils. In University of Port-Harcourt Teaching Hospital, there is a practice of taking surface swab of palatine tonsils for microscopy, culture and sensitivity to guide antimicrobial therapy which may not reflect the core pathogens. There may be a difference between surface and core aerobic bacteriology of adenoid and tonsils hence this study. Aim: To compare surface versus core aerobic bacteria of adenoid and tonsillar tissues in children undergoing adenotonsillectomy at University of Port-Harcourt Teaching Hospital. Materials and Methods: This was a hospital based cross-sectional study involving fifty(50) paediatric participants aged 3-7years undergoing adenotonsillectomy. Informed consent was sought from patient’s caregiver and a pretested proforma was used to recruit the participants for the study. Surface swabs of the tonsils and adenoid were taken following general anaesthesia and orotracheal intubation in the theatre. The core tissue specimens of adenoid and tonsils were collected after adenotonsillectomy. The core specimens and surface swabs were sent immediately to microbiology laboratory for processing. Isolation of bacteria by Gram staining and biochemical testing was done, followed by susceptibility testing and beta-lactamase production detection. Results were analyzed using the Statistical Product and Service Solutions (SPSS) version 20. Pearson’s chi square statistics was used to determine the difference in the bacteriology between the surface and core of the adenoid and tonsils. A p-value of less than 0.05 was considered statistically significant. Results: In the demographic characteristics of the study group, age range less ...