BACKGROUND Palatine tonsils are the components of Mucosa Associated Lymphoid Tissue (MALT) of pharynx. Embryologically, they develop from second branchial arch and play an important role in immune system. These are lined by stratified squamous epithelium in continuation with pharyngeal mucosa. The surface epithelium of tonsil will invaginate to form crypts. These crypts contain cheesy material which constitute food debris, keratin and bacteria. Infection of tonsil, tonsillitis was a more common infection of humans. During tonsillitis, the bacteria inhabiting the crypts will multiply and secrete toxins. This inflammation of tonsil tissue will lead to WBC infiltration, finally leading to swollen and congested tonsils. Antibiotics play an important role in treatment of acute tonsillitis. Appropriate antibiotic selection from tonsil surface swab culture for an adequate duration will prevent the continuation and spread of infection. Contrary to this surface swab culture oriented antibiotic selection, few studies reported that the bacteria causing tonsillitis may also be present in deep tonsillar tissues. Hence, the organisms grown from tonsillar surface swab cultures may not be representative of actual infective organism always. MATERIALS AND METHODS This descriptive study was carried out as a prospective study among 60 patients who underwent tonsillectomy at a tertiary care hospital. Data was collected about various socio-demographic factors, clinical information and details about routine lab examinations. After tonsillectomy, the specimen was transferred in sterile water for aerobic culture and KOH mount. RESULTS Out of 33 positive cultures, S. aureus (48.5%) was grown majorly followed by H. influenzae (18.2%), S. pyogenes (12.1%), Pseudomonas (9.1%), K. pneumoniae (6.1%), S. pneumoniae (3%) and no fungal elements were detected. CONCLUSION Surface cultured microorganism represent more of normal commensals, which is a false indicator of the pathogen in the core. The findings of this study are in support of directing rational therapy against tonsillar core pathogens like Staph. aureus, H. influenza, Pseudomonas, Klebsiella with antibiotics like Gentamycin, Amikacin and Ciprofloxacin.