A common motif in otolaryngology is the lack of certainty regarding diagnosis for middle ear conditions, resulting in many patients being overtreated under the worst-case assumption. Although pneumatic otoscopy and adjunctive tests offer additional information, white light otoscopy has been the main tool for diagnosis of external auditory canal and middle ear pathologies for over a century. In middle ear pathologies, the inability to avail high-resolution structural and/or molecular imaging is particularly glaring, leading to a complicated and erratic decision analysis. Here, we propose a novel multiwavelength fluorescence-based video-rate imaging strategy that combines readily available optical elements and software components to create a novel otoscopic device. This modified otoscope enables low-cost, detailed and objective diagnosis of common middle ear pathological conditions. Using the detection of congenital cholesteatoma as a specific example, we demonstrate the feasibility of fluorescence imaging to differentiate this proliferative lesion from uninvolved middle ear tissue based on the characteristic autofluorescence signals. Availability of real-time, wide-field chemical information should enable more complete removal of cholesteatoma, allowing for better hearing preservation and substantially reducing the well-documented risks, costs and psychological effects of repeated surgical procedures.