Autonomic regulation of cardiac activity during stress has not been clearly defined in farm animals. In part, this is due to the limited availability of affordable ambulatory cardiac monitors capable of accurately monitoring and storing large amounts of data that meet the criteria necessary for heart rate variability analysis. Our objectives were to measure the accuracy of a 24-h Polar RR monitor using gold standard ECG, to examine and categorise any occurring anomalies and to ascertain their impact on the outcome of heart rate variability analysis. Five 1-year-old female pigs (gilts) were socially isolated from their pen mates and cardiac activity was simultaneously measured using two systems, a 24-h Polar RR Recorder and a Telemetric ECG system. The Polar data were manually assessed both against and in isolation of the ECG data to identify anomalous beats, which were then assigned to one of five identified error categories. The anomalies in the Polar data were corrected and statistical comparisons were performed among the three data sets to evaluate the effects of anomalies on heart rate variability analysis. Bland-Altman analysis was used to measure the level of agreement among the ECG, Uncorrected Polar and Corrected Polar data. No anomalies or ectopies were found in the ECG data but 46 anomalies (0.81% of total interbeat intervals [IBI]) were found in the Polar Uncorrected data. Manual identification and editing procedures reduced this error to 0.018%. Most mean heart rate and IBI parameters were unaffected by error (P>.05). Standard deviation (S.D.) and root mean square of successive differences (RMSSD) were 45% and 50% higher when anomalies were present in the data. Artefacts affected the magnitude of the frequency domain indices and overestimated total and parasympathetic activity and underestimated sympathetic activity. The mean difference between ECG and Uncorrected Polar data was 1.36 ms (limits of agreement -69.03 to 71.74 ms). This was greatly improved to 0.36 ms (limits of agreement -5.37 to 6.10 ms) after editing. Overall, even a small proportion of error biased the outcome of heart rate variability analysis. This bias was greatly reduced by correcting the anomalous beats. Bland-Altman analysis demonstrated that when there was error present in the Polar data, it could not be used interchangeably with the ECG data. However, if there were no anomalies present in the data or if they were classified and corrected using the approach in this study, then the two systems could be used interchangeably.