This report describes the results of a cross-sectional anonymised online survey on adherence to, and side effects from oseltamivir when offered for prophylaxis, among pupils from one primary and two secondary schools with confirmed cases of influenza A(H1N1)v in London in April-May 2009. Of 103 respondents (response rate 40%), 95 were estimated to have been offered oseltamivir for prophylaxis, of whom 85 (89%) actually took any. Less than half (48%) of primary schoolchildren completed a full course, compared to three-quarters (76%) of secondary schoolchildren. More than half (53%) of all schoolchildren taking prophylactic oseltamivir reported one or more side effects. Gastrointestinal symptoms were reported by 40% of children and 18% reported a mild neuropsychiatric side effect. The results confirmed anecdotal evidence of poor adherence, provided timely information with which to assist decision-making, and formed part of the body of growing evidence that contributed to policy changes to restrict widespread use of prophylaxis for school contacts of confirmed cases of influenza A(H1N1)v.