Object： Detecting of disease spread is an important task of public health and medical staff, especially in pandemics such as A/H1N1 flu (2009). This requires daily observation and estimation of the infected population. The fully automated real-time pharmacy survey we developed collects information electronically at pharmaceutical prescription. We used the data to analyze the pandemic A/H1N1 flu spread (2009) and to determine the systemʼs and capability in estimating the infected population. Method： Automatic collection of prescription information on anti influenza virus drugs from 3,959 pharmacies provided the basis for calculating the number of influenza sufferers and determining shape of the epidemic curve compared to that of official influenza sentinel surveys and mandatory reports of A/H1N1 (2009) patients. We also compared infection estimates from the pharmacy survey to those of official sentinel survey and a one-week survey of all hospitals and clinics in Gifu prefecture not reported in sentinel. Results： Fully automated real-time pharmacy surveillance began on April 20, 2009, and provided feedback at 07 : 00 daily. It estimated the infected population at 22,708 when official sentinel surveillance recorded an average of 0.99 influenza visits per week in epidemic week 32 when publicly announced that the pandemic had began in Japan. By the end of March, epidemic week 12 in 2010, infected-population estimates totaled 9,234,289, and peaked on November 24 at 234,519 in one day. All A/H1N1 (2009) sufferers reported mandatorily until mid-July numbered 25,526.The pharmacy survey indicated that there were influenza nationalwide by the time the very first outbreak emerged in the Kansai (western Japan) area. The correlation coefficient for the pharmacy and official sentinel survey was 0.992 nationwide, exceeding 0.95 in which only 33 of Japanʼs 47 prefectures were counted. The estimated infected population in the pharmacy survey was half of that of the official sentinel survey. The pharmacy survey yielded almost the same number as the complete survey in Gifu prefecture, however. Discussion： Fully automated real-time pharmacy surveys are useful in long-term observation e.g. detection of rapid emergence, identifying the peak, and careful monitoring of reemergence. It was demonstrated as the leading indicator for the official sentinel surveillance because of high correlation among them. Information collected daily is very useful in early detection and estimating the affected population. The survey consistently uses the same estimation criterion and operates automatically and routinely, facilitating the comparison of the latest and past results. The pharmacy survey indicated that official sentinel survey estimates overestimate actual cases and thus require modification to ensure accuracy. The pharmacy survey thus appears to be very valuable as a tool in measuring for the second wave of A/H1N1 (2009) or whatever the next pandemic may be. It can, of course, be applied to diseases other than influenza, e.g. varicella, by following antivaricellazostervirus prescriptions and antibiotic drugs.