The main objective of this study is to find the correlation and differences between the microflora isolated and characterized from the surface and core regions of the tonsils, where the subjects were initially defined as tonsillitis. The maximum age incidence was from 6 to 12 years where the sex incidence was more in females than males. In majority of the patients, jugulodigastric nodes are palpable where the squeeze test was positive to 22% of cases. Sore throat and odynophagia are the symptoms predominantly found and these were presented with 2 to 3 years of duration among maximum cases, where in the average duration was 1 year and 7 months. Majority of the patients had chronic parenchymatous tonsillitis but enlarged adenoids were the most commonly associated ENT condition. Among the bacterial isolates, 87% was possible to aerobic isolation whereas 13% possibility was for both aerobic and anaerobic bacterial members. In the surface region, β haemolytic streptococci and Staphylococcus aureus are predominant isolates whereas in core region, β haemolytic streptococci and Streptococcus pneumoniae are possible. The variations in the bacterial isolates were possible maximum in core region compared to surface. Bacteriodes was the common anerobe found in both core and surface but dominance of Fusobacterium was identified in surface area only. The raised ASO titre was found in majority of the patients. Norfloxacin and ciprofloxacin are the common and routine antibiotic classically found effective against the isolates that re-establishing the superiority of the newer generation antibiotics to traditional penicillin.