The objective of this study was to evaluate the association between cow-specific risk factors and the lactational incidence risks of retained placenta (RP), metritis (MET) and clinical mastitis (CM) in 57,301 dairy cows on 20 large dairy herds in Iran between January 2005 and June 2009. A multivariable logistic regression model was used to identify risk factors for MET, RP and CM and quantify their odds ratio (OR). The lactational incidences of MET, RP and CM were 8%, 5.2% and 18.9%, respectively, and significant risk factors for MET were dystocia (OR = 4.32), stillbirth (OR = 6.26), RP (OR = 27.74), twin births (OR = 6.57), primiparity (OR = 1.68), calving during winter season (OR = 2.45) and male calves (OR = 2.41). Significant risk factors for RP were dystocia (OR = 3.17), stillbirth (OR = 3.18), abortion (OR = 8.46), milk fever (OR = 3.66), twin births (OR = 2.76), pluriparity (OR = 2.69), calving during winter season (OR = 1.86) and shorter gestation length of dairy cows (OR = 3.82). Also, significant risk factors for CM were RP (OR = 9.45), milk fever (OR = 12.36), pluriparity (OR = 2.83), calving during winter season (OR = 1.68) and the first months of lactation (P < 0.001)) and SCC concentrations at previous lactation (OR = 1.82). The current study indicates that differentiation can be made among cows in the risk of having MET, RP and CM based on a combination of cow factors. These differences among cows could be useful to aid the better detection of these diseases in the dairy herds.