The objective of this study was to investigate the effects of puerperal uterine disease on uterine blood flow using trans-rectal Doppler sonography. Lactating Holstein Friesian cows (n = 44) were divided into two groups based on whether they were healthy (UD−; n = 23) or had uterine disease (UD+; n = 21) defined as retained fetal membranes and/or metritis. General clinical examination, vaginoscopy, trans-rectal palpation, and trans-rectal B-Mode sonography were conducted on Days 8, 11, 18, 25 and then every 10 days until Day 65 after calving. Doppler sonography of the uterine arteries was conducted on Day 8, during diestrus after the second ovulation (Days 40–60 after calving) and during diestrus before breeding (Days 63–75 after calving). Cows with uterine disease had greater (P < 0.05) uterine size as assessed trans-rectally compared with cows of the UD group. Sonographic measurements on Day 11 after parturition revealed a greater (P < 0.05) horn diameter in cows of the UD+ than in the UD− group. Both uterine size and uterine horn diameter decreased more earlier following parturition (P < 0.05) in cows of the UD− group. Blood flow volume (BFV) was greater and pulsatility index was less on Day 8 after calving in cows of UD+ than UD− group (P < 0.05). In cows of the UD−, but not in those of the UD+ group, there was a further reduction in BFV subsequent to Day 45 after calving (P < 0.05). The results of this study show that uterine blood flow measures by trans-rectal Doppler sonography are affected by puerperal uterine disease.