Previous studies have shown that influenza A virus inoculated via a transbullar approach can cause severe disorders of the chinchilla eustachian tube. In this study, we inoculated chinchillas both intranasally and transbullarly with influenza A virus (A/Alaska/6/77) to assess the effect of this virus on both the ciliary activity of eustachian tube epithelium and eustachian tube transport function. Data indicated that while the nature of the major lesions was indistinguishable, the differing routes of inoculation did influence the time course and initial location of virus-induced histopathology. Analysis of ciliary beat frequency and dye transport function indicated a maximal decrease approximately 7 to 14 days postinoculation, with return to normal function by 28 days postinoculation. Light and transmission electron microscopic observations of the evolution of histopathology and return to normal histology correlated well with functional assessment data.