The 2009 novel H1N1 influenza pandemic had a significant impact on Shenzhen's population with 2063 laboratory-confirmed human H1N1 cases and five deaths being reported. We used parameters from two population-based surveys and the Shenzhen Influenza Surveillance System to estimate the total number of H1N1 influenza infections in Shenzhen in the 2009 pandemic. The attack rate of influenza-like illness (ILI) in family households was 11·2% (95% CI 9·4–13·0), with 80·2% (95% CI 77·8–82·5) seeking medical care. The ILI attack rate in workers was 38·1% (95% CI 34·3–41·7) with 72·5% (95% CI 66·9–78·0) seeking medical care. The average H1N1 positive rate in individuals reporting ILI and testing by polymerase chain reaction was 22·7%. A total of 611 000–768 000 people, or 4·7–5·9% of the Shenzhen population, are estimated to have experienced H1N1 influenza. The estimated total number of cases of H1N1 is likely to be 330 times greater than the number of laboratory-confirmed cases.