Bottlenose dolphins were submitted to structural (CT) and functional (SPECT/PET) scans to investigate their in vivo anatomy and physiology with respect to structures important to hearing and echolocation. The spatial arrangement of the nasal passage and sinus air spaces to the auditory bullae and phonic lips was studied in two dolphins via CT. Air volume of the sinuses and nasal passages ranged from 267.4 to 380.9 ml. Relationships of air spaces to the auditory bullae and phonic lips support previous hypotheses that air protects the ears from echolocation clicks generated by the dolphin and contributes to dolphin hearing capabilities (e.g. minimum angular resolution, inter-aural intensity differences). Lung air may replenish reductions in sinus and nasal passage air volume via the palatopharyngeal sphincter, thus permitting the echolocation mechanism to operate at depth. To determine the relative extent of regional blood flow within the head of the dolphin, two dolphins were scanned with SPECT after an intravenous dose of 1850 MBq 99mTc-bicisate. A single dolphin received 740 MBq of 18F-2-fluoro-2-deoxyglucose (FDG) to identify the relative metabolic activity of head tissues. Substantial blood flow was noted across the dorsoanterior curvature of the melon and within the posterior region of the lower jaw fats. Metabolism of these tissues relative to others within the head was nominal. It is suggested that blood flow in these fat bodies serves to thermoregulate lipid density of the melon and jaw canal. Sound velocity is inversely related to the temperature of acoustic lipids (decreasing lipid density), and changes in lipid temperature are likely to impact the wave guide properties of the sound projection and reception pathways. Thermoregulation of lipid density may maintain sound velocity gradients of the acoustic lipid complexes, particularly in the outer shell of the melon, which otherwise might vary in response to changing environmental temperatures.