The aim of this study was to clarify the site of primary pathology in otitis media with effusion. Effusions were collected from 64 children with bilateral effusions at the time of myringotomy. The rheological properties and biochemical compositions of effusions were measured for 23 pairs of effusions, and the levels of the inflammatory mediators TNF alpha, IL-1beta, and IL-8 were measured in 41 pairs using specific enzyme-linked immunosorbent assays (ELISAs). Measurements from paired ears were compared using analysis of variance (ANOVA) tests and significant differences were found for reduced specific viscosity, mucin content, protein content, and levels of IL-8. The results demonstrate that the two ears have different immunological processes or rates of processes which might explain the significantly different rheological properties of effusions. This suggests that each ear undergoes pathological changes independently and has implications for using the opposite ear as a control in clinical trials.