This study was carried out on 71 lactating Holstein Friesian cows to investigate the resumption of ovarian cyclicity postpartum and the reproductive performance in cows carrying the mutation of complex vertebral malformation (CVM) compared with control ones. The cows were distributed in two dairy farms in Hiroshima Prefecture, Western Japan. Blood samples were collected from the cows to detect carrier cows with CVM mutation. Furthermore, plasma samples were collected weekly after calving from control cows (n = 10) and CVM carrier cows (n = 10), until 10 weeks postpartum to investigate the day of first ovulation and the resumption of ovarian cyclicity postpartum. The reproductive parameters were investigated and compared with control and CVM carrier cows. Thirty-six cows were diagnosed to be CVM carriers by DNA examination and confirmed later by DNA sequencing. The pedigree analysis of the carrier cows revealed that they were daughters of six types of CVM carrier semen that still was used in dairy farms in Western Japan. In terms of reproductive indices, there were no significant differences between the control and the CVM carrier cows on the day of the first ovulation postpartum and the interval from calving to first insemination. However, CVM carrier cows significantly required more inseminations per conception and showed a significantly longer period to conception and subsequent calving than control ones. In conclusion, the reproductive performance of the CVM carrier cows was lowered through conception failure that might indicate the occurrence of intra-uterine mortality in those cows.