BackgroundHeart rate variability (HRV) parameters, and especially RMSSD (root mean squared successive differences in RR interval), could distinguish atrial fibrillation (AF) from sinus rhythm(SR) in horses, as was demonstrated in a previous study. If heart rate monitors (HRM) automatically calculating RMSSD could also distinguish AF from SR, they would be useful for the monitoring of AF recurrence. The objective of the study was to assess whether RMSSD values obtained from a HRM can differentiate AF from SR in horses. Furthermore, the impact of artifact correction algorithms, integrated in the analyses software for HRV analyses was evaluated. Fourteen horses presented for AF treatment were simultaneously equipped with a HRM and an electrocardiogram (ECG). A two-minute recording at rest, walk and trot, before and after cardioversion, was obtained. RR intervals used were those determined automatically by the HRM and by the equine ECG analysis software, and those obtained after manual correction of QRS detection within the ECG software. RMSSD was calculated by the HRM software and by dedicated HRV software, using six different artifact filters. Statistical analysis was performed using the Wilcoxon signed-rank test and receiver operating curves.ResultsThe HRM, which applies a low level filter, produced high area under the curve (AUC) (> 0.9) and cut off values with high sensitivity and specificity. Similar results were obtained for the ECG, when low level artifact filtering was applied. When no artifact correction was used during trotting, an important decrease in AUC (0.75) occurred.ConclusionIn horses treated for AF, HRMs with automatic RMSSD calculations distinguish between AF and SR. Such devices might be a useful aid to monitor for AF recurrence in horses.Electronic supplementary materialThe online version of this article (10.1186/s12917-018-1650-6) contains supplementary material, which is available to authorized users.