Subclinical mastitis in heifers during early lactation affects udder health, future milk production and, therefore, the risk of premature culling. The aim of this cross-sectional study was to identify pre- and post-partum risk factors associated with a high heifer mastitis rate (HMR), and to find out which period (either pre- or post-partum) contains more risk factors and consequently should be the focus of mastitis control in heifers. A total of 77 herds were included in this study and the potential animal- and farm-related risk factors were recorded during a one-time farm visit. The HMR was provided by the dairy herd improvement test (DHI) as the annual average of the past 11 DHIs. For this study, data were analyzed in two models using generalized linear models. Each model examined the association between possible risk factors and HMR, one including only prepartum risk factors and the other one only post-partum risk factors. One identified pre-partum risk factor was the proportion of udder-healthy cows in the herd. Post-partum risk factors were the type of teat cleaning procedure before milking, teat disinfection, treatment of mastitis in heifers, a body condition score (BCS) of >3.0 in fresh heifers, and the combination of a teat cleaning procedure with a teat disinfectant. The results show the importance of the period shortly after calving for udder health in heifers, as four of the five significant risk factors were identified in this period and three of them were related to the milking process. However, further research with a higher number of herds is needed to minimize individual herd effects.