Historically, the foramen magnum (FM) has been an integral component of studies on skull ontogeny and evolutionary transformations of cranial form. Although this foramen has been considered a single entity, we hypothesize that it comprises two functional matrices, a ventral matrix and a dorsal matrix. In general, the ventral matrix is related to locomotor functions, whereas the dorsal matrix is related to neurological functions and fluid flow dynamics. To test our hypothesis, we used a large ontogenetic sample of modern human crania (seventh fetal month to adult) to (1) delineate bony size and shape ontogeny for both the foramen and its dorsal and ventral units; (2) delineate the role of synchondroses in the observed growth patterns and rates; and (3) explore the relationship between FM and cranial size, shape, and growth. Detailed growth patterns and rates are established for the bony FM and its ventral and dorsal skeletal units. These data are supplemented by literature and observational data on embryonic and fetal FM ontogeny, soft tissue relationships, anomalous/pathological extremes of size, and craniocervical anatomy and locomotor functions. The hypothesis that the FM is composed of a ventral and a dorsal functional matrix is supported by observed ontogenetic differences between ventral and dorsal skeletal units, as well as by the soft tissue anatomy of these matrices. Further documentation of these matrices has the potential to significantly enhance our understanding of the ontogenetic and evolutionary transformations of skull base morphology. Anat Rec, 2011. © 2010 Wiley-Liss, Inc.