Lactational strategies and associated development of the young have been studied in a diverse range of species, and comparative analysis allows common trends and differences to be revealed. The whey fraction contains a vast number of proteins, many of which have not been assigned a function. However, it is expected that an understanding of the comparative biology of these proteins may provide some promise in assigning a function to the major whey proteins. Whey acidic protein is a major component of the whey fraction that has been studied across a range of species, revealing conservation of gene structure, whereas regulation and temporal expression patterns vary. This review focuses primarily on comparative analysis of whey acidic protein, highlighting gene structure, developmental and hormonal regulation, and potential functional roles for this protein. In addition, the contrasting regulation and secretion profiles of several other major whey proteins are discussed.