Variation in vertebrate cranial morphology is both extensive and functionally significant. Morphometric analysis attempts to explain such variation in form in evolutionary and functional contexts. Developmental morphometric analyses of vertebrate crania are less common, and many taxa are underrepresented. For example, the published morphometric studies of crocodilian cranial development focus mainly on posthatchling head development, with few, incomplete morphometric analyses of prehatchling heads. To further explore ontogenetic changes in the alligator head, we recorded and analyzed six linear cranial measurements in 77 preserved embryonic and hatchling American alligators (Alligator mississippiensis) representing 20 different stages. Examination of individual measurements revealed nonlinear changes in growth rate during development, suggesting a level of dynamic complexity worthy of further analysis. Using principal components analysis, we identified three distinct phases in prenatal alligator head growth. The second (intermediate) phase disrupts an otherwise monotonic developmental trajectory and represents a phase of reduced snout growth. Although this is a detailed description of prehatchling ontogenetic trajectory of the alligator head, further studies in other crocodilians are needed to assess evolutionary patterns among crocodilians.