Mouse models have been widely used to elucidate the biology of mammary gland development and secretory activation. Recent advances in the availability of genomic resources for mice will generate a renewed effort to define the genetic basis of lactation phenotypes and help identify candidate gene pathways. Specific aspects of these advances are relevant to the dairy industry and may provide a rationale for improving milk production in the dairy cow. Differences are evident in mammary gland morphology and various characteristics of milk production of inbred mouse strains, but few studies have undertaken any systematic phenotypic analysis of the different inbred strains of mice for lactation performance. Whole genome association analysis using recent strain-specific genotype data and detailed phenotype measurements from available inbred strains, along with transcript profiling of divergent inbred strains for lactation performance, provides a valuable approach to identify putative candidate genes and associated pathways underlying dairy QTL intervals. Here we discuss the utility of integrating mouse phenomic and genomic resources for understanding secretory activation in the mammary gland.