Hepatic gene expression during the transition period is dynamic and responsive to changes in hormones, nutrients, and fatty acids (FA). Concentration and profile of FA differs postpartum between cows diagnosed with hyperketonemia (HYK) or not (nonHYK). The objectives were to determine hepatic gene expression and the relationship between FA profile and gene expression in HYK and nonHYK cows. Cows were enrolled 28 d before calving. Plasma samples were collected at −3, 1, 3, 7, 9, 11 and 14 d and liver biopsies at 1, 14 and 28 d. Postpartum plasma samples were analyzed for BHB and nonesterified FA. Fatty acid profile (−3, 1, 14 d) was determined via acid methylation and GC. Cows were classified as HYK (BHB ≥ 1.2 mM postpartum; average onset ± SD, 9 ± 5 d; n = 13) or nonHYK (BHB < 1.2mM; n = 15). Liver was analyzed for FA profile and expression of pyruvate carboxylase (PC) and cytosolic phosphoenolpyruvate carboxykinase (PEPCKc) quantified by real time PCR, analyzed by standard curve method, and normalized to ribosomal protein L32 (6 reference genes explored with geNORM). Data were analyzed in SAS 9.4 using PROC MIXED containing the fixed effects of time [repeated cow(HYK)], HYK, and time × HYK. Time × HYK affected PC (P = 0.01) with HYK cows having decreased PC on d1 (0.94 vs. 0.33 ± 0.08 arbitrary units [AU]; P < 0.01) but not d14 (0.18 vs. 0.13 ± 0.08 AU; P = 0.74) or 28 (0.28 vs. 0.08 ± 0.08 AU; P = 0.12). Abundance of PEPCKc was not affected by HYK (P = 0.28) or time × HYK (P = 0.87). This resulted in decreased PC:PEPCKc on d 1 (P = 0.01), but not d 14 or 28 (P > 0.10), suggesting decreased complete oxidative capacity at parturition in cows that later develop HYK. The decreased PC in HYK cows at d 1 was not correlated with differences in nonesterified FA concentration or FA profile (P > 0.10). These data support that there are differences in PC:PEPCKc at calving in cows with subsequent HYK; however, shifts in FA profile do not appear to be related to downregulation of PC at d 1 in cows that subsequently develop HYK. Ultimately, the decreased PC:PEPCKc at parturition may contribute to onset of HYK and the regulatory mechanism should be further examined.