The domestic dog (Canis familiaris) has been shown to both excel in recognising human emotions and produce emotion-related vocalisations and postures that humans can easily recognise. However, little is known about the effect of emotional experiences on subsequent sleep physiology, a set of phenomena heavily interrelated with emotions in the case of humans. The present paper examines heart rate (HR) and heart rate variability (HRV) during dogs’ sleep, measures that are influenced by both positive and negative emotions in awake dogs. In Study I, descriptive HR and HRV data is provided on N = 12 dogs about the different sleep stages (wake, drowsiness, non-rapid eye movement (non-REM), REM; scoring based on electroencephalogram (EEG) data). We conclude that wakefulness is characterised by higher HR and lower HRV compared to all sleep stages. Furthermore, drowsiness is characterised by higher HR and lower HRV than non-REM and REM, but only if the electrocardiogram (ECG) samples are taken from the first occurrence of a given sleep stage, not when the longest periods of each sleep stage are analysed. Non-REM and REM sleep were not found to be different from each other in either HR or HRV parameters. In Study II, sleep HR and HRV measures are compared in N = 16 dogs after a positive versus negative social interaction (within-subject design). The positive social interaction consisted of petting and ball play, while the negative social interaction was a mixture of separation, threatening approach and still face test. Results are consistent with the two-dimensional emotion hypothesis in that following the intense positive interaction more elevated HR and decreased HRV is found compared to the mildly negative (lower intensity) interaction. However, although this trend can be observed in all sleep stages except for REM, the results only reach significance in the wake stage. In sum, the present findings suggest that HR and HRV are possible to measure during dogs’ sleep, and can potentially be used to study the effect of emotions not only during but also after such interactions.