This paper describes a web-based system developed to collect data on influenza (flu) vaccine uptake in near real time during the flu season in England. Data are collected from all GP practices providing the immunisation programme. Data are submitted either monthly or weekly on-line to a website using manual, automated and semi-automated methods. During the 2008/09 season, a final response rate of 96.2% was achieved (n=7980/8293). This equates to 52,217,430 GP registered patients aged 6 months and over being included in the survey. The majority of reports (65.5%) were submitted via automated or semi-automated methods. We were also able to collect the data weekly from a sentinel group of GP practices (approximately 50%) that have fully automated data extraction facilities. This system successfully provides data locally and nationally to monitor the annual seasonal flu programme, with a large sample size, quickly and efficiently, with minimal burden on the NHS. At a time when the first influenza pandemic of the 21st century is occurring, the ability to measure influenza vaccine uptake coverage in near real time will be invaluable.