Objective: Mastitis is defined as the inflammation of the mammary gland, which impact directly on the production performance and welfare of dairy cattle. Since, mastitis is a multifactorial complex disease and the molecular pathways underlying this disorder have not been clearly understood yet, a system biology approach was used in this study to a better understanding of the molecular mechanisms behind mastitis. Methods: Publicly available RNA-Seq data containing samples from milk of five infected and five healthy Holstein cows at five time points were retrieved. Gene Co-expression network analysis (WGCNA) approach and functional enrichment analysis were then applied with the aim to find the non-preserved module of genes that their connectivity were altered under infected condition. Hub genes were identified in the non-preserved modules and were subjected to protein-protein interactions (PPI) network construction. Results: Among the 25 modules identified, eight modules were non-preserved and were also biologically associated with inflammation, immune response and mastitis development. Interestingly most of the hub genes in the eight modules were also densely connected in the PPI network. Of the hub genes, 250 genes were hubs in both coexpression and PPI networks and most of them were reported to play important roles in immune response or inflammatory pathways. The blue module was highly enriched in inflammatory responses and STAT1 was suggested to play an important role in mastitis development by regulating the immune related genes in this module. Moreover, a set of highly connected genes were identified such as BIRC3,