Cortical granules (CGs) are secretory vesicles associated with egg and oocyte plasma membranes that undergo exocytosis at fertilisation. In the sea urchin Strongylocentrotus purpuratus, the internal organisation of these CGs exhibits a lamellar-type morphology. The different lamellar layers correspond to proteoglycans, structural proteins and enzymes required for fertilisation envelope assembly and modification of the post-fertilisation egg surface. We have studied the lamellar structure of CGs using X-ray scattering and reveal the contrast density variation of the lamellae in the native state. The structure of functionally competent CGs in situ differs significantly from that determined by electron microscopic studies. We observed a strong periodicity of the lamellar structure of 280 A as opposed to the 590 A repeat observed previously. Fusion of the CGs produced a loss of the lamellar repeat and the development of a broad peak corresponding to a 20 A periodicity that may be indicative of the molecular packing in the resulting hydrated gel structure.