Antibiotics are frequently prescribed when a diagnosis of acute otitis media (AOM) is made in childhood, but the effects of antibiotics on host-parasite interactions in the middle ear are not well defined. A rat model and PCR techniques were used to explore host responses during amoxicillin treatment of AOM caused by non-typeable Haemophilus influenzae (NTHi). The 5 day course of amoxicillin initiated at the otomicroscopic peak of the infection eradicated the bacteria and induced significant changes in the expression of cytokines. Interleukin (IL)-6, tumour necrosis factor-alpha and IL-10 were upregulated by the treatment, and the downregulation was slower than during the natural course. Amoxicillin inhibited the upregulation of transforming growth factor-beta, whereas IL-1alpha expression remained unaffected by the treatment. By comparing inflammatory host responses during treated and untreated NTHi AOM, new targets for modification of the course, or more specified and individualized treatments, may evolve.