Background: Chronic tonsillitis is most common condition which affects school going children. Improper use of antibiotic among the common population has led to many drug resistant organisms; therefore, it is necessary to study the antimicrobial susceptibility pattern before treating the patient with Chronic tonsillitis. Aim of the study is to determine whether fine-needle aspiration of tonsil, gives a representative picture of deep tonsil flora in chronic tonsillitis, as assessed by subsequent culture from the core of the resected tonsils, and to compare the findings of fine needle tonsils aspiration, with findings from a routine superficial tonsil surface swab. Methods: Study conducted at ENT department of Vinayaka mission medical college, Karaikal, Pondicherry over a period of 1year (June 2018 to May 2019). 77 patients were operated for chronic tonsillitis were included in the study. 3 swabs were collected from surface of tonsil. Tonsil aspiration was done using a 10-mL syringe with an18-gauge needle and swab from core of tonsil was collected for culture and sensitivity. Bacterial isolates were identified using standard methods and antibiotic susceptibility testing were done. Results: Group B hemolytic streptococcus, Streptococcus pneumonae and Staphlococcus aueus were the predominant microbes isolated in the aspirate and tonsil core tissue in outpatient population. Whereas Alpha hemolytic streptoccus and Group B hemolytic streptococcus were predominantly seen in tonsillar surface. Conclusions: Tonsil fine needle aspiration helps in diagnosis of Chronic tonsillitis and culture based antibiotic therapy. Due to which Tonsillectomy procedures can be avoided in Chronic tonsillitis patients.