Acute tonsillitis is a common childhood disease, but repeated antibiotic treatment may fail, leading to tonsillectomy. Superficial swab cultures do not sufficiently represent the core bacteria present, but fine-needle aspiration may be a promising diagnostic method. We evaluated 58 patients undergoing tonsillectomy, and took superficial and core swabs, and fine-needle aspirations. Staphylococcus aureus was the most common bacterial pathogen identified, present in 26 out of 50 (52%) positive core cultures, followed by Haemophilus influenza in 13 positive core cultures (26%), and group A beta-haemolytic streptococci in 10 positive core cultures (20%). Fine-needle aspiration detected 33 out of 50 positive core cultures (66%), whereas superficial swab culture detected 18 of 50 (36%); the difference being statistically significant. All pathogens detected by superficial swabs and fine-needle aspiration were detected in core cultures. The sensitivity and specificity of fine-needle aspiration were 66% and 100%, respectively, compared with 36% and 100% for superficial swabs. Fine-needle aspiration is therefore a promising method for detecting core bacteria in patients with recurrent tonsillitis.