Context: Osteopathic physicians have used osteopathic manipulative medicine (OMM) to treat patients with acute otitis media (AOM) and its sequelae (eg, middle ear effusion [MEE], conductive hearing loss) for more than a century. However, few clinical trials document the efficacy of OMM, perhaps because of various challenges related to OMM clinical trials.Objectives: To describe a research protocol studying the efficacy of OMM on MEE after an episode of AOM, comment on the feasibility of the protocol and statistical analysis, and report on lessons learned in the first 9 months of the study.Methods: Dual-site, prospective, randomized, blinded, controlled clinical trial comparing OMM plus standard care to standard care only for MEE after an episode of AOM. Standard care comprised antibiotics and surgery. Patients were aged between 6 months and 24 months, were diagnosed as having AOM, were referred to the study by a participating pediatric provider, and had abnormal tympanogram results on entry into the study. All patients had 5 weekly study visits, and patients in the intervention group received OMM on visits 1 through 3. Patients received weekly tympanogram and acoustic reflectometer readings as well as daily at-home acoustic reflectometer readings for 30 days.Results: Fifty-six patients were screened, 34 subjects were enrolled, and 26 subjects completed the study protocol in the first 9 months of the study. This resulted in 22 “ears” in the standard card only group and 18 “ears” in the standard care plus OMM group, resulting in 40 cases of AOM studied in the first year of the trial. The OMM treatment protocol was easily administered without serious adverse events. Protocols for interpretation of tympanogram readings and conversion of data for statistical analysis resulted in analyzable data.Conclusions: The OMM protocol can be administered with no serious adverse events. Subject recruitment is difficult, and a full-time research assistant at the referring site improves subject referral, enrollment and retention. Accepting only confirmed cases of AOM from trained pediatric providers reduces the patient pool but increases the reliability of the data. (ClinicalTrials.gov number NCT00520039)