Head nods are a frequently observed phenomenon by both Japanese users and Japanese Sign Language (JSL) users. However, while head nods used in spoken Japanese are a part of a paralinguistic feature, previous sign language studies show that head nods in JSL function as an important linguistic element. Among several functions of head nods, this study investigates the mechanism of head nods as a prosodic marker, occurring at Intonational Phrase (IP) boundaries. Four native Japanese speakers, four native JSL Deaf signers, and three non-native certified JSL interpreters participated in this study, and their use of prosodic head nods were compared regarding the frequency of occurrence at IP boundaries and the timing of the head nod nucleus (the lowest head nod position). The result shows that while the frequency of head nods at IP boundaries shows individual variation among Japanese speakers, the Deaf JSL signers systematically show prosodic head nods at IP boundaries in a consistently high rate. Also, a different timing of the head nod nucleus is observed between Japanese and JSL. As for the comparative analysis between the Deaf JSL signers and non-native JSL interpreters, the data reveals that the use of prosodic head nods by non-native interpreters is not as inconsistent as that of Deaf native signers, suggesting that Japanese head nod behavior would affect JSL interpretation by non-native JSL interpreters to some degree.