Shenzhen is one of the largest migratory metropolitan cities in China. A standardized influenza surveillance system has been operating in Shenzhen for several years. The objectives of the present study were to describe the epidemiology of influenza in Shenzhen and to assess the impact of pandemic H1N1 on influenza activity. An average rate of 71 cases of influenza-like illness (ILI)/1000 consultations was reported, which was greater than the rate in the preceding 3 years. Laboratory surveillance showed that the annual proportion of specimens positive for influenza was 25·4% in 2009, representing a significant increase over the proportions of 5·4%, 11·6% and 12·2% in 2006, 2007 and 2008, respectively. A total of 414 ILI outbreaks were reported in 2009, which was a marked increase compared to the previous 3 years. Influenza activity reached a record high in Shenzhen in 2009. Seasonal A/H3N2 was the dominant strain during the summer and was gradually replaced by pandemic H1N1. A semi-annual cycle for influenza circulation began to appear due to the emergence of pandemic H1N1.