The present study was undertaken to develop an improved cryoembedding method for analysis of mice and rat cochleae, which permits high-quality cryosections and preserves overall structure and cellular resolution as shown by hematoxylin/eosin staining. The preservation of morphology and antigenicity is mandatory to achieve optimal results. A total of 20 male cd/1 mice and 14 male Sprague-Dawley rats were used in experiments for optimization of preservation, fixative, decalcification, embedding and cryosectioning of cochleae from adult and aged rodents. In addition, a novel immunohistochemical procedure (using Hydroxyprobe-1 kit) was developed for detecting regions of hypoxia in mice and rat cochlea. This method employs a primary fluorescent-conjugated monoclonal antibody directed against pimonidazole protein adducts that are created in hypoxic tissues. Subsequent studies of hypoxia inducible factor-1alpha (HIF-1alpha) by immunofluorescence in the cochlea of these animals were performed in order to confirm that immunochemical detection of pimonidazole protein is representative of a hypoxic environment. We conclude that the present method results in high-quality cryosections of cochlear tissues presenting good anatomical and histological preservation. Furthermore, our optimized procedures provide novel tools for the investigation of neuro-sensory-epithelium in physio-pathological situations associated with hypoxia and/or ischemia, such as inner ear development, plasticity, regeneration and senescence.