Increased energy demands to support lactation, coupled with lowered feed intake capacity results in negative energy balance (NEB) and is typically characterised by extensive mobilisation of body energy reserves in the early postpartum dairy cow. The catabolism of stored lipid leads to an increase in the systemic concentrations of non-esterified fatty acids (NEFA) and beta hydroxy butyrate (BHB). Oxidation of NEFA in the liver result in the increased production of reactive oxygen species (ROS) and the onset of oxidative stress and can lead to disruption of normal metabolism and physiology. The immune system is depressed in the peripartum period and early lactation and dairy cows are therefore more vulnerable to bacterial infections causing mastitis and or endometritis at this time. A bovine Affymetrix oligonucleotide array was used to determine global gene expression in the spleen of dairy cows in the early post-partum period. Spleen tissue was removed post mortem from five severe NEB (SNEB) and five medium NEB (MNEB) cows 15 days post-partum. SNEB increased systemic concentrations of NEFA and BHB and white blood cell and lymphocyte numbers were decreased in SNEB animals. A total of 545 genes were altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with NRF2 mediated oxidative stress, mitochondrial dysfunction, endoplasmic reticulum stress, natural killer cell signalling, p53 signalling, down-regulation of IL-15, BCL-2 and IFN; up-regulation of BAX and CHOP and increased apoptosis with a potential negative impact on innate and adaptive immunity.