There is a high incidence of infectious and metabolic disease in the transition period. During this time, there is a period of observed immunosuppression that appears to be ‘natural’. The effect of parturition on neutrophil function is of particular interest; we hypothesized that neutrophil dysfunction occurs around the transition period, as evidenced by altered gene expression. To determine this, we extracted neutrophils from peripheral blood of 45 cows at 5 time points: 1 wk pre-calving (−1 wk), day of parturition (d 0), and post-calving at wk 1, 2, and 4. Key pathways of neutrophil function were investigated by qRT-PCR. The ‘bovine immune panel’ (BIP) included 96 targets for detection with Fluidigm 96.96 integrated fluidic circuits and the Biomark HD system. Data were analyzed using SAS 9.3; the effect of time was analyzed using a mixed model approach to repeated measures ANOVA and Tukey’s t-test for pairwise comparisons between weeks. Data were submitted for pathway enrichment analysis using the protein analysis through evolutionary relationships tool. The top 3 pathways enriched from gene targets on the BIP included inflammation signaling (14-fold enrichment, P < 0.001), apoptosis signaling (19-fold enrichment, P < 0.001), and interleukin/cytokine signaling (18-fold enrichment, P < 0.001). Biological processes enriched at −1 wk, d 0, and 1 wk post-calving included the immune system process, response to stimulus, and the immune response. The immune response process was most highly enriched (8-fold enrichment, P < 0.05) at 1 wk post-calving, which coincided with greatest NEFA concentration (1.08 ± 0.52) and, therefore, greatest NEB. No biological processes were enriched at 2 wk or 4 wk post-calving. Results indicate that the gene expression profile of neutrophils is altered over the transition period. This provides insight into neutrophil activity around parturition and the increased susceptibility to disease during this time.