This study tests the hypothesis that high levels of high-frequency heart rate variability (HF-HRV) predisposes individuals to affiliate with new groups. Resting cardiac physiological recordings were taken before and after experimental sessions to measure trait high-frequency heart rate variability as an index of dispositional autonomic influence on heart rate. Following an experimental manipulation of priming of caring-related words, participants engaged in a minimal group paradigm, in which they imagined being a member of one of two arbitrary groups, allocated money to members of the two groups, and rated their affiliation with the groups. High levels of HF-HRV were associated with ingroup favouritism while allocating money, an effect largely attributable to a positive relationship between HF-HRV and allocation of money to the ingroup, and less due to a negative relationship between HF-HRV and money allocation to the outgroup. HF-HRV was also associated with increased self-reported affiliation feelings for the ingroup but was unrelated to feelings towards the outgroup. These effects remained substantial even after controlling for age, gender, BMI, mood, caffeine consumption, time of day of data collection, smoking and alcohol behaviour, and respiration rate. Further, the effects were observed regardless of whether participants were primed with caring-related words or not. This study is the first to bridge a long history of research on ingroup favouritism to the relatively recent body of research on cardiac vagal tone by uncovering a positive association between HF-HRV and affiliation with a novel group.