School-age children are at a high risk of acute respiratory virus infections including the 2009 pandemic influenza A(H1N1). School absence records have been suggested as a tool for influenza surveillance. We analysed absence records from six primary schools (children aged from around five to 11 years) in London during the years 2005 to 2007 in order to provide baseline epidemiological characteristics of illness-related school absence, and to correlate school absence with seasonal influenza. The daily average prevalence of absence due to illness was 2.9%. The incidence was 1.3% per person-day. The mean duration of absence was 1.8 days (SD 1.8). Over 60% of absence episodes lasted for one day. Absence prevalence did not differ by sex. Prevalence was highest in the youngest children and then declined slightly, but was again high again in the oldest. Absence was slightly higher on Mondays and Fridays. In general, peaks of absenteeism coincided with peaks of influenza A and B (laboratory reports) but several high peaks were not associated with influenza. There was a better correlation between absence and laboratory reports and prevalence compared to incidence. School absence data may be useful for the detection of localised school outbreaks and as an additional surveillance tool but are limited by lack of data on weekends and during holidays.