To analyze the relationship of blood metabolite concentrations and body condition score (BCS) with persistent bacterial uterine infection, specifically that caused by Trueperella pyogenes and anaerobic bacteria, uterine bacteriological swabs (n = 128) were collected from 64 Holstein cows at 5 (W5) and 7 (W7) weeks postpartum, and the percentage of neutrophils in the endometrium was evaluated. Blood glucose, total cholesterol (T-cho), blood urea nitrogen (BUN), non-esterified fatty acid (NEFA), and β-hydroxybutyric acid concentrations were analyzed at 3 weeks (W-3) and 1 week (W-1) prepartum and W3, W5, and W7 postpartum. BCS were evaluated at W-3, W3, and W7. Blood glucose concentrations at W-3 and W-1 in cows with persistent bacterial infection were lower (P = 0.05) than in the rest of the cows. Total BUN concentrations in cows with persistent bacterial infection were lower (P < 0.01) than those in other cows, although the association between the pre or postpartum time and status of infection was not significant. Total NEFA concentrations in cows with persistent bacterial infection were similar to those in uninfected cows and cows positive for infection at W5 but not W7. Total BCS in cows with persistent bacterial infection were lower (P < 0.01) than those in cows positive for infection at both W5 but not W7 and W7 but not W5; however, the association between the pre or postpartum time and status of infection was not significant. Glucose concentrations at W-3 and W-1 negatively correlated with persistent bacterial infection at W5 and W7 (P < 0.01). BUN concentrations at W3 (P < 0.01), W5 (P < 0.05), and W7 (P < 0.05) and BCS at W3 (P < 0.01) negatively correlated with persistent postpartum bacterial infection. Decreased prepartum blood glucose concentrations might be an important risk factor for persistent postpartum bacterial uterine infection in dairy cows.