Little is known of the molecular regulation of human milk production because of limitations in obtaining mammary tissue from lactating women. Our objectives were to evaluate whether RNA isolated from breast milk fat globules (MFGs) could be an alternative to mammary biopsies and to determine whether intense breast pumping, which increases prolactin (PRL) secretion, will upregulate alpha-lactalbumin (alpha-LA, a major determinant of lactose synthesis) transcription. RNA was isolated from MFG and transcripts of interest were identified and quantitated by real-time RT-PCR using an external standard for normalization. In addition, we performed microarray studies to determine MFG RNA gene expression profile. Ten lactating women were studied using two protocols: protocol A with intense pumping from 0800 to 0814 h followed by short pumping and protocol B with intense pumping from 1200 to 1214 h preceded by short pumping. Plasma PRL and MFG alpha-LA mRNA expression were measured. During protocol A, plasma PRL (61+/-7-248+/-43 mug/l by 14 min) and alpha-LA (3.5+/-0.9 fold by 6 h; P<0.03) increased. During protocol B, PRL gradually increased over 4 h from 69+/-14 to 205+/-28 mug/l, and further to 329+/-23 mug/l by 12 min of intense pumping; alpha-LA mRNA expression did not increase significantly. We conclude that MFGs provide a unique source to study the in vivo regulation of gene expression in mammary epithelial cells. alpha-LA mRNA is abundant in the MFG and its expression may be regulated by hormonal and temporal factors.