An animal’s external head morphology is the starting point of auditory communication by receiving sounds from the environment and plays an especially important role in how an animal perceives and localizes sounds. Particularly, the presence of the external ear structure, or pinna, is essential to front/back and vertical discrimination of acoustic signals. The process of accurately perceiving the location of acoustic signals is not only reliant on morphology but also on deeper processing at the brainstem level. For the brain to assess the approximate location of a sound, it relies on the computation of two cues: interaural time differences (ITDs), which can be defined as the shift in arrival time of a particular sound at each of the pinnae, and interaural level differences (ILDs), or the shift in sound level of a particular sound at each of the pinnae (i.e., sounds coming from the left side of an individual are going to be perceived slightly quicker and as slightly louder at the left ear versus the right ear). Therefore, it is assumed that significant variability in head and pinna size and shape will also cause significant variability in the detection of acoustic signals. In this study, we focus on identifying differences in external head and pinna morphology in six species of North American deer mice (genus Peromyscus) to determine if there are differences in head morphology based on species distribution differences. We measured the dimensions of the head and pinna of over 1,200 preserved specimens of P. boylii, P. californicus, P. gossypinus, P. leucopus, P. maniculatus, and P. truei, followed by a series of head-related transfer functions (HRTFs) on several individuals to study the relationship between morphology and auditory function. Our results show the greatest variability in inter-pinna distance and pinna width across the six species with similar ITDs and ILDs, suggesting that differences in morphology may be more related to discriminating elevation of sounds, not differences in horizontal sound discrimination. Not only will this study contribute to existing research on external morphology and auditory function, but it will also provide invaluable insight into the use of preserved specimens in auditory research, an area that is currently understudied.