The microbial flora of 75 patients with chronic tonsillitis were sudied to identify the commonest organism causing chronic tonsillitis and to compare surface swab, fine needle aspiration (FNA) and core swab in isolating the pathogens. Staphylococcus aureus was the predominant isolate from surface core swab FNA and surface swab. In our study the correlation between surface swab with core swab was 47.9% and between surface swab with FNA 57.3%. The correlation between FNA with core swab of 69.3% showed that FNA for culture was superior to surface swab in predicting the core culture. Hence FNA of the tonsil has more advantage over the routinely performed surface swab in representing the core pathogen. Thus the rationale of treating chronic tonsillitis medically should be based on the knowledge of the common core pathogen.