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The uterine lumen in early postpartum dairy cows is contaminated with different bacteria. The most relevant uterine pathogens are Escherichia coli and Trueperella pyogenes. Prevalence of α-hemolytic streptococci and coagulase-negative staphylococci (CNS) is also high; however, these pathogens are considered opportunistic. The overall objective of this study was to investigate effects of the intrauterine presence of E. coli, T. pyogenes, α-hemolytic streptococci, or CNS at 10±1 d in milk (DIM) on the type of bacteria 2 wk later and their influence on uterine infections and subsequent reproductive performance. Furthermore, we set out to quantify 2 relevant methodological factors (i.e., laboratory and sampling instrument). Bacteriological samples were collected at 10±1 and 24±1 DIM from the uterine lumen using a cytobrush (CB). Vaginal mucus was classified by vaginoscopy. In a subsample, bacteriological results of 3 different laboratories and of CB and cotton swabs (CS) were compared. Samples of uterine discharge were collected at 10±1 DIM and bacteriological samples were taken using CB and CS. Bacteria were identified and bacterial growth quantified on a 4-point scale. Animals infected with E. coli or T. pyogenes at 10±1 DIM had a higher risk for an infection with the same bacterial species at 24±1 DIM [E. coli relative risk (RR)=3.7 and T. pyogenes RR=2.9]. Moreover, the risk of being diagnosed with abnormal vaginal discharge at 24±1 DIM increased in cows with E. coli (RR=1.7) or T. pyogenes (RR=1.7) at 10±1 DIM. Uterine infection with α-hemolytic streptococci or CNS did not increase the risk of an infection with T. pyogenes or E. coli or abnormal vaginal discharge 2 wk later. Cows with E. coli at 10±1 DIM or T. pyogenes at 24±1 DIM had greater days to first artificial insemination than cows positive for the 3 remaining bacterial species. Cows with T. pyogenes at 10±1 DIM had more days to pregnancy and more cows were culled when positive for E. coli at 10±1 DIM. Agreement of bacteriological results of 3 different laboratories were significant for laboratory A + B and A + C for the CB and CS. The highest agreement considering the bacterial species was for E. coli. All results for laboratory A + B and A + C for the CB and CS were significant. The results generated from samples collected with CB agreed nicely with those from CS from each laboratory (laboratory A: 250/272; laboratory B: 264/272; laboratory C: 253/272).