This study assessed the interchangeability between heart rate (HR) and heart rate variability (HRV) measures derived from a series of interbeat intervals (IBIs) recorded via electrocardiogram (ECG) and intra-arterial blood pressure (BP) in various behavioral contexts. Five minutes of simultaneously recorded IBIs from ECG and BP signals in 11 female domestic pigs during resting, feeding and active behavior were analyzed. Comparisons were made for measures of HR, SDNN (the standard deviation of IBIs) and RMSSD (the root mean of the squared distances of subsequent IBIs) derived from ECG and BP signals for each behavior category using statistical procedures with different explanatory power (linear regression, intraclass correlation coefficient (ICC), Bland and Altman plots and analysis of variance (ANOVA)). Linear regression showed a strong relationship for HR during all behaviors and for HRV during resting. Excellent ICCs (lower 95% CI > 0.75) and narrow limits of agreement (LoA) in all behavior categories were found for HR. ICCs for HRV reached the critical lower 95% CI value of 0.75 only during resting. Using Bland and Altman plots, HRV agreement was unacceptable for all of the behavior categories. ANOVA showed significant differences between the methods in terms of HRV. BP systematically overestimated HRV compared with ECG. Our findings reveal that HR data recorded via BP agree well those recorded using ECG independently of the activity of the subject, whereas ECG and BP cannot be used interchangeably in the context of HRV in free-moving domestic pigs.