Social grooming is assumed to have both social and hygienic functions. In monkey species, body site preferences during social grooming are related to both the dominance ranks of participating individuals and strength of social bonds. It is suggested that low-ranking groomees and individuals with weak social bonds expose less vulnerable sites of their body because doing so allows them to avoid eye contact, thus reducing the risk of aggression. This study aimed to investigate the influence of (1) the levels of affiliation (through analyses of sex, grooming frequency, and group membership during intergroup encounters), (2) dominance, (3) kinship, and (4) age on grooming site preferences (head, front, back, anogenital region, and limbs) in wild bonobos. Subjects were two groups of wild bonobos living in Wamba, DR Congo. Body site preferences were documented from video clips. Our results illustrate that the levels of affiliation between individuals and their dominance status do not seem to influence body site preferences, contrasting with results in monkey species. However, the selection of body sites was mostly influenced by age and kinship. Mothers were found to groom less accessible sites on their immature offspring's body more than when grooming a non-related immature, suggesting that mothers invest in their offspring more to prevent diseases linked to ectoparasites. Finally, mature individuals groomed the inaccessible back more often than immature individuals, while the latter focused their grooming on the head and front. Overall, this study suggests hygienic functions of social grooming in wild bonobos.