An outbreak of influenza A occurred in a prison system in New South Wales, Australia in January 2003 during the southern hemisphere summer. This report documents only the third confirmed outbreak of influenza in a prison environment. The outbreak investigation included case ascertainment, state-wide surveillance, a case-control study and interventions to limit the outbreak such as infection control, quarantine, cohorting of cases, and the use of antiviral medication for prophylaxis. A total of 37 clinical cases were identified. Influenza A virus was detected in 11 of the 22 respiratory tract specimens collected. The virus was typed as an influenza A/Fujian/411/2002 (H3N2)-like virus. This strain subsequently became the predominant virus strain during the northern hemisphere winter and the following 2003 Australian southern hemisphere winter influenza season.