The mammalian upper respiratory tract is a functionally dynamic region involved in respiration, deglutition, and phonation. As the structures of this area (e.g., larynx, hyoid) are suspended from the basicranium, changes in basicranial shape may affect both their anatomy and function. Although skeletal/soft tissue relationships have been examined through descriptive, comparative anatomy, these relationships have remained largely unexplored via experimental study. In this study, mechanical relationships between basicranial shape and positions of the larynx and hyoid bone are investigated experimentally. Skull base flexion was induced by surgically ablating the spheno-occipital synchondrosis in 13-day-old rats. Lateral radiograms were taken at 40, 60, 80, 100, and 120 days, and angular measurements made of basicranial shape and positions of the larynx and hyoid bone. Statistical analysis shows significant differences between experimental and control groups for skull base, hyoid, and larynx angles, and negative (inverse) correlations for basicranial shape change vs. hyoid position, and basicranial shape change vs. larynx position. Results show induced basicranial flexion caused inferior displacement of the larynx and hyoid bone, thus indicating a direct, mechanical relationship between skeletal and soft tissues. These observations may aid in understanding the basic biological, pathological, and evolutionary interactions of hard and soft tissues of the upper respiratory region.