At the heart of the skim milk system are the colloidal casein-calcium-transport complexes termed the casein micelles. The application of physical chemical techniques such as light, neutron, and X-ray scattering and electron microscopy has yielded a wealth of experimental detail concerning the structure of the casein micelle. From these experimental data bases have arisen two conflicting models for the internal structure of the casein micelle. One model emphasizes protein submicellar structures as the dominant feature, while the other proposes that inorganic calcium phosphate nanoclusters serve this function. These models are critically examined in light of our current information regarding the biological processes of protein secretion. In addition two primary tenets of structural biology are applied: that protein structure gives rise to function and that competent protein-protein interactions (associations) will lead to efficient transit through the mammary secretory apparatus. However, a set of complex equilibria governs this process which may be completed only after the final step in the processes: milking. In this light an overwhelming argument can be made for the formation of proteinacious complexes (submicelles) as the formative agents in the synthesis of casein micelles in mammary tissue. Whether these submicelles persist in the milk has been questioned. However, perturbations in micellar equilibria allow for the reemergence of submicellar particles in dairy products such as cheese. Thus protein-protein interactions appear to be important in milk and dairy products from the endoplasmic reticulum to the cheese cutting board.