In the present study, to clarify the causes of lower fertility in cows with ipsilateral relationship of the first wave dominant follicle and corpus luteum in the same ovary, we analyzed the amounts of endometrium mRNA by real-time PCR and postpartum metabolic status by milk yield and milk components between ipsilateral group (IG) and contralateral group (CG). Amounts of PGR、PGRMC1、ESR1、PGFS and PPARA mRNA were higher in CG than IG. Negative energy balance of postparum status was more severe in IG than CG. From these results, it is possible that the cows with more severe negative energy balance lead the ipsilateral relationship of the first wave dominant follicle and corpus luteum in the same ovary. Also, it is speculated that the difference of amounts of mRNA in endometrium were caused by difference of postpartum metebolic status.