The tonsils are lymphoid organs that act as sentinels for the nasopharyngeal region and can be prone to recurrent infection, particularly throughout early childhood. The goal of this study was to determine whether the tonsil TCR Vb repertoire showed skewing indicative of the presence of bacterial superantigens (SAg). Bacterial SAg are typically associated with life-threatening illnesses such as Toxic Shock Syndrome, but may also drive milder conditions such as chronic rhinosinusitis. Tonsils were donated by patients undergoing a tonsillectomy due to recurrent tonsillitis (RT) or Obstructive Sleep Apnoea (OSA).Both the tonsil surface and tissue were cultured for bacteria, particularly Staphylococcus aureus and Group A Streptococcus (GAS) that often secrete SAg. The tonsillar CD4+ and CD8+ TCR Vb repertoire was assessed by flow cytometry. Skewing of the TCR Vb repertoire was determined by identifying values that were >2 standard deviations higher than established reference values. To date S. aureus has been recovered from 15/26 (58%) and GAS from 3/26 (11.5%) of patients. Skewing of the TCR Vb repertoire was identified in 9/26 (34%) of patients and strikingly S. aureus was cultured from 8 of these patients, most of whom had RT. The possible association between S. aureus and skewing of the TCR Vb repertoire was unexpected as GAS is considered to be an important driver of RT. If a causal association between S. aureus, expression of SAg and RT can be established, this may change treatment approaches for this illness.