AbstractIn long bone development, the evolution of the cartilaginous anlagen into a secondary ossification center is initiated by the formation of canals. The excavation to create the canals is achieved through lysis of the two major cartilage components, aggrecan, and the type II collagen (COL2) fibril. The present study examines the lysis of the fibril. Because it is known that matrix metalloproteinases (MMPs) cleave COL2 in vitro at the Gly775‐Leu776 bond, it has been reasoned that, if such cleavage is detected in relation to the canals, it can be concluded that a collagenase is involved. Furthermore, because MMPs undergo change in domain structure with activation resulting in propeptide domain loss then, if such a loss is revealed in relation to the cleavage of COL2, this MMP is likely involved. The collective findings reveal that COL2 is attacked at the afore‐described susceptible peptide bond at the surface of cartilage canals and, that MMP‐13 cleaves it. Developmental Dynamics 238:1547–1563, 2009. © 2009 Wiley‐Liss, Inc.