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Fifty-three patients were enrolled and evaluable in a randomized, double-blinded controlled clinical trial comparing prednisone for 7 days plus trimethoprim-sulfamethoxazole (TMP/SMZ) for 30 days vs. TMP/SMZ alone in treating chronic middle ear effusion (MEE). Clearing of the effusion in both ears or in one when only one was involved was called complete resolution; clearing in one of two effected ears was called partial resolution. The outcomes 2 weeks after initiation of therapy of 26 patients initially treated with prednisone plus TMP/SMZ were complete resolution in 20, partial resolution in three, and unchanged in three. The outcomes in 27 patients initially treated with TMP/SMZ alone were complete resolution in eight, partial resolution in three, unchanged in 13 and development of acute otitis media in three (P<0.01 for complete resolution). Two weeks after initiation of therapy, patients with a MEE that failed to clear were crossed over to the alternative regimen. Overall 29 of 41 patients (71%) who received oral prednisone plus TMP/SMZ initially or after the crossover had complete resolution of their middle ear effusion at 2 weeks after starting prednisone and TMP/SMZ. Five of 35 (14%) patients treated with prednisone plus TMP/SMZ and one of six (17%) patients treated with TMP/SMZ alone who had complete resolution at 4 weeks required subsequent referrals for tympanostomy tubes. A course of prednisone for 7 days plus TMP/SMZ for 30 days with monthly follow-up should be considered in children with MEE persisting beyond 6–8 weeks before referral for tympanostomy tube placement.