Many influenza-like illness (ILI) outpatients visit healthcare facilities such as internal medicine and pediatric clinics every year. In Japan, however, ILI is reported only by sentinel healthcare facilities. We studied the number of ILI subjects visiting sentinel and non-sentinel healthcare facilities during the 2008-09 season in Saku, Nagano prefecture, obtaining the numbers of cases from sentinel and non-sentinel facilities. Most ILI subjects visited internal and pediatric facilities, and some visited otorhinolaryngological clinics not included as sentinel sites. We also estimated the total number of influenza cases based on data from sentinel facilities and total surveyed facilities, including non-sentinel. We divided facilities into hospitals with pediatrics, pediatric clinics, internal medicine and pediatric clinics, hospitals and clinics with internal medicine but no pediatrics, and otorhinolaryngological clinics. Estimated sentinel-site ILI cases was 2862, including 1020 for hospitals with pediatrics and 1,674 for clinics with internal medicine and pediatrics. The estimated number of ILI cases from total facilities surveyed was significantly lower, at 503 for hospitals with pediatrics, and 741 for clinics with internal medicine and pediatrics. Estimated ILI cases from categories not including sentinel sites were 967 for hospitals and clinics with internal medicine but no pediatrics, and 71 for otorhinolaryngological clinics. The estimated number of total ILI cases differed by 18.5%, depending on facility categories. This indicates that more detailed analysis is needed to accurately estimate ILI cases.