ABSTRACT.Our objective was to conduct a genome-wide association study on cow mortality and 305-d milk yield for three lactations and determine if there were differences in the genetic architecture in three US regions. Genomic EBV of mortality and milk yield were estimated with a single-step genomic BLUP using a threshold-linear model. Genomic information was included on 34,506 bulls. Data consisted of the entire US data and three regions SE: southeast, SW: southwest, and NE: northeast for first three lactation cows calving from 1999 to 2008. As expected, a segment on chromosome 14 was significantly associated with milk production in all regions. Chromosome 14 showed a strong association with the first parity mortality for the entire US, with NE showing a strong association for all three parities. Within SE and SW regions, no single region stood out for mortality on chromosomes for three parities.