Reproductive performance is paramount to efficient milk production in dairy cows. Many postpartum cows do not clear uterine inflammation and resume normal ovarian cyclicity by the time they are presented for reinsemination. This dissertation aimed to study of factors associated with the delay in clearance of uterine inflammation and resumption of ovarian cyclicity in the postpartum cow. Subclinical endometritis (SCE) is the presence of inflammation in the uterus beyond the normal involution without any other signs of disease. A large epidemiological study was performed obtaining uterine samples, risk factors and reproductive outcome data from 38 commercial dairy herds. Cow-level risk factors for SCE identified were: ketosis, milk production and metritis. Reagent strip test was evaluated as a potential cow-side test for SCE. Reagent strip tests were found to be strongly associated with SCE, however low sensitivity and specificity limits its potential use. The effects uterine sample collections on economically important outcomes on sampled cows were tested and no detrimental effects were found. The main difference between early postpartum follicles that will ovulate and those that do is the ability to produce a rise in circulating estradiol concentrations. A novel follicle fate prediction method was used to identify cows that will likely go on to ovulate or not using follicle growth parameters and circulating estradiol concentrations. This allowed for follicular fluid collection and steroid hormone analyses. In non-ovulatory cows; the theca cell function was impaired, there were fewer luteinizing hormone pulses, and had more severe negative energy balance primarily due to decreased feed intake compared with ovulatory cows. Uterine health association with follicular function was evaluated. Certain bacterial isolates were associated with reduced follicle growth. Follicular fluid endotoxin levels were found to be higher in non-ovulatory cow and they also had higher circulating haptoglobin levels which are an indicator for acute phase response. Negative energy balance and uterine health disorders were associated with both SCE and non-ovulation