Early pregnancy loss is a major reason for low reproductive efficiency in the horse. In humans and mice, low numbers of regulatory T cells (Treg cells) are linked to miscarriage. The percentage of Treg cells in oestrous mares at the start of the breeding season was evaluated in relation to the outcome of subsequent pregnancy. For identification and quantification of Treg cells, a highly sensitive and specific qPCR assay targeting the Treg-specific demethylated region in the equine forkhead box transcription factor (FOXP3) gene was established. In a total of 108 mares, pregnancy was followed until detection of early pregnancy loss (n=17), abortion without identification of an infectious or apparent cause (n=9) or birth of a viable foal (n=82). Measured Treg-cell levels did not significantly differ between mares that conceived (82%; 1.50±0.04%) or did not get pregnant (18%; 1.45±0.10%). The Treg-cell percentage at oestrus before breeding was significantly different (P<0.05) between mares that either underwent early pregnancy loss up to Day 40 of pregnancy (1.29±0.07%) and mares that aborted (1.61±0.15%) or gave birth to a live foal (1.52±0.05%). These results suggest that low levels of Treg cells in mares can contribute to pregnancy loss up to Day 40 after ovulation.