Milk fever (MF) is an important metabolic disorder of dairy cows around the time of calving. MF leads to important economic losses due to deaths, reduction in milk production and productive lifespan, as well as costs associated with both prevention and treatment. The objective of this study was to unravel the genomic architecture underlying MF in Holstein dairy cattle. Data consisted of 28k producer-recorded MF event records from 14k cows. The analysis included a whole-genome scan to identify genetic variants and genes regulating MF, and a subsequent gene set analysis for detecting pathways and biological mechanisms associated with MF. The association analysis identified several regions located on BTA6, BTA7, BTA14, BTA16, BTA17, and BTA23 that explained a significant amount of genetic variance for MF. These regions harbor several genes; for example, GC, CAMK2A, CAMK1G and CPNE5, that are directly involved in calcium and vitamin D metabolism. Notably, these regions also harbor microRNAs that regulate the expression of genes implicated in calcium ion transmembrane transport, such as CACNA1D and NCS1. Moreover, the gene set analyses revealed several significant functional categories, including endorphins, potassium channels, phosphatidylinositol phosphates, and NFATC transcription factors. Most of these terms are associated either with hypocalcemia or the cascade of events that occur during MF. Overall, our study contributes to a better understanding of the genetic control of this complex disease. These findings can provide opportunities for improving MF in dairy cattle through marker-assisted selection.