This study compares the microbial profiles obtained from tonsil surface culture, tonsil core culture, and adenoid core culture in pediatric patients with recurrent adenotonsillitis. Conducted at a tertiary care center in Chennai, Tamil Nadu over two years, the study enrolled pediatric patients (5-18 years) diagnosed with recurrent adenotonsillitis undergoing tonsillectomy with or without adenoidectomy. Throat swabs were collected preoperatively for culture and sensitivity, and a preoperative dose of Inj. Amoxicillin with Clavulanic acid was administered. Tissue samples obtained during surgery were subjected to aerobic culture and sensitivity analysis. A total of 91 patients were included in the study. None of the throat swabs yielded pathogenic organisms, while 91% and 80% of the tonsil and adenoid cores yielded growth on culture, respectively. The most common organisms isolated from tonsil and adenoid core cultures were Streptococcus species and Enterococcus. In 62% of cases, the same organism was obtained from both tonsil and adenoid cores, while it differed in 11% of cases. No growth was observed in 10% of cases. The antibiotic sensitivity profile showed that Ciprofloxacin was the drug to which most organisms were susceptible. This study highlights the microbial diversity within tonsillar and adenoidal tissues in pediatric patients with recurrent adenotonsillitis. Understanding these patterns can aid in optimizing the management strategies and improving patient outcomes.