Objective To determine the long term effects of antibiotic treatment for acute otitis media in young children. Design Prospective three year follow-up study within the framework of a primary care based, double blind, randomised, placebo controlled trial. Setting 53 general practices in the Netherlands. Participants 168 children aged 6 months to 2 years with acute otitis media. Interventions Amoxicillin 40 mg/kg/day in three doses compared with placebo. Main outcome measures Recurrence of acute otitis media; referral to secondary care; ear, nose, and throat surgery. Results Acute otitis media recurred in 63% (47/75) of children in the amoxicillin group and in 43% (37/86) of the placebo group (risk difference 20%, 95% confidence interval 5% to 35%); 30% (24/78 amoxicillin; 27/89 placebo) of children in both groups were referred to secondary care, and 21% (16/78) of the amoxicillin group compared with 30% (27/90) of the placebo group had ear, nose, and throat surgery (risk difference −9%, −23% to 4%). Conclusion Recurrent acute otitis media occurred more often in the children originally treated with amoxicillin. This is another argument for judicious use of antibiotics in children with acute otitis media. Trial registration Netherlands Trial Register NTR1426.