Many countries now have guidelines on the clinical management of acute otitis media. In almost all, the public health goal of containing acquired resistance in bacteria through reduced antibiotic prescribing is the main aim and basis for recommendations. Despite some partial short-term successes, clinical activity databases and opinion surveys suggest that such restrictive guidelines are not followed closely, so this aim is not achieved. Radical new solutions are needed to tackle irrationalities in healthcare systems which set the short-term physician-patient relationship against long-term public health. Resolving this opposition will require comprehensive policy appraisal and co-ordinated actions at many levels, not just dissemination of evidence and promotion of guidelines. The inappropriate clinical rationales that underpin non-compliance with guidelines can be questioned by evidence, but also need specific developments promoting alternative solutions, within a framework of whole-system thinking. Promising developments would be (a) physician training modules on age-appropriate analgesia and on detection plus referral of rare complications like mastoiditis, and (b) vaccination against the most common and serious bacterial pathogens.