The objectives of this study were to conduct genome-wide association studies (GWAS) on conception rate (CR), production traits, and SCS for Holstein cows and determine if the genetic architecture of these traits is different in 3 stages of lactation for the first 3 parities in US Holsteins. Genome-wide association studies were conducted for conception rate (CR), test-day milk, fat and protein yields, and test-day SCS. The data were split into 3 sets: early (<14wk), middle (14wk ≤ DIM ≤ 29wk), and end (29wk < ). Heritability estimates for CR were lowest (0.03) in the middle and highest (0.05 to 0.08) in the end of lactation in all parities. Genetic correlations of CR with other production traits were low and all negative (−0.1 to −0.5). The SNP marker effects were divided into equal segments of 30 SNP. A segment on chromosome 14 was associated with CR only in early and middle stages of lactation in the third parity; the proportion of the total genetic variance explained by this segment for CR were 2.7% and 2.5%, respectively. The proportions for test-day milk and fat yields were highest in the middle of lactation (7% for milk and 8% for fat) in all 3 parities, whereas the proportions for test-day protein and SCS were low (<2%). The results suggest that gene expression for CR and milk production traits is stronger in early and middle lactation stages and similar over the lactations.