Cows experiencing severe postpartal negative energy balance (NEB) are at greater risk of developing mastitis than cows in positive energy balance (PEB). Our objectives were to compare mammary tissue gene expression profiles between lactating cows (n = 5/treatment) subjected to feed restriction to induce NEB and cows fed ad libitum to maintain PEB in order to identify genes involved in immune response and cellular metabolism that may predispose cows to an intramammary infection in non-infected mammary gland. The NEB cows were feed-restricted to 60% of calculated net energy for lactation requirements, and cows fed PEB cows were fed the same diet ad libitum. At 5 days after feed restriction, one rear mammary gland from all cows was biopsied for RNA extraction and transcript profiling using microarray and quantitative PCR. Energy balance (NEB vs. PEB) resulted in 278 differentially expressed genes (DEG). Among up-regulated DEG (n = 180), Ingenuity Pathway Analysis® identified lipid metabolism (8) and molecular transport (14) as some of the most enriched molecular functions. Genes down-regulated by NEB (98) were associated with cell growth and proliferation (21) and cell death (18). Results indicate that DEG due to NEB in mid-lactation were associated with numerous biological functions but we did not identify genes that could, a priori, be associated with risk of intramammary infection in non-infected mammary glands. Further studies with early postpartal cows are required.