Acute otitis media (AOM) is a common bacterial infection in childhood that causes an inflammatory response in the middle ear. Leukocytes produce different inflammatory molecules in vitro when stimulated with Gram-positive and Gram-negative bacteria. The major causes of AOM are Streptococcus pneumoniae, nontypeable Haemophilus influenza, and Moraxella catarrhalis. We sought to assess differences in cytokines, chemokines, and expression of Toll-like receptors (TLRs) at onset of AOM based on bacterial culture results. Middle ear fluid (MEF) from 66 children with AOM was studied. Innate immune genes, cytokines (interleukin [IL]-6, IL-8, IL-10, IL1-β; tumor necrosis factor-α), chemokines (CCL2, CCL3, CCL4, CCR5, CXCR3), and Toll-like receptors (TLR2, TLR4, TLR9) expression was measured using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) from MEF collected in vivo by tympanocentesis. Culture-positive MEF had higher levels of all cytokines and chemokines (9-300-fold) as compared to MEF that was culture negative. Polymerase chain reaction (PCR)-positive/culture-negative MEF for otopathogens showed significant differences (P < .01) in TLR2, TLR4, and TLR9 expression (6-31-fold), but cytokine and chemokine levels were similar compared to PCR-negative/culture-negative MEF. No significant differences were found in the cytokine/chemokine/TLR levels among the bacterial otopathogen species. However, higher levels of TLRs, and all the cytokine and chemokines were detected when more than one bacterial species was present compared to single otopathogens. Expression levels of proinflammatory cytokines/chemokines and TLRs are elevated in AOM children with a bacterial otopathogen, and are dependent on the number of bacterial species identified.