Between May and September each year, influenza sentinel surveillance is conducted in general practices in Melbourne and the state of Victoria in southern Australia. We describe the first 11 weeks of sentinel surveillance in 2009 (weeks 18-28), during which time pandemic influenza (H1N1) 2009 virus became established, and investigate the protective effect of seasonal influenza vaccine against laboratory-confirmed infection caused by the pandemic virus. At the time of reporting, the peak ILI activity in 2009 had been reached and was similar to the peak recorded in 2007 but below the peak of 2003. The proportion of cases positive for any influenza virus increased from 6% in the first week of surveillance (week 18) to 59% by week 28, during which time the proportion of influenza viruses detected as pandemic influenza increased from zero to 95%, with at least 91% of all influenza viruses confirmed as pandemic influenza by the eighth week of surveillance (week 25). The median age of all 223 patients with pandemic influenza for whom age was known was 21 years (range 2-63 years) compared with the median age of 53 patients with seasonal H1N1 influenza in 2007 or 2008 of 23 years (range 1-75 years). There was no evidence of significant protection from seasonal vaccine against pandemic influenza virus infection in any age group.