To assess the association between influenza immunization and subsequent diagnosis of group A streptococcus (GAS)-illness in Army recruits during influenza seasons 2002-2006. A case-control study was employed with cases as trainees with outpatient GAS diagnosis (ICD-9-CM codes: 034.0, 035, 038.0, 041.01, 320.2, 390-392, 482.31) during the influenza season, and controls as trainees with no outpatient GAS diagnosis during the influenza season. Primary exposure was influenza immunization during 1st September to 30th April of each season. Estimated protective effects of influenza immunization against GAS-illness ranged from 50% to 77%. A strong protective effect was suggested for Army trainee influenza immunization on the diagnosis of GAS-illness.