Role of host factors in transmission of human papillomavirus (HPV)-infection from mother to her offspring is not known. Our aim was to study whether human leukocyte antigen (HLA)-G allele concordance among the mother–child pairs could facilitate vertical transmission of HPV, because HLA-G may contribute to immune tolerance in pregnancy. Altogether, 310 mother-child pairs were included from the Finnish Family HPV study. Overall, nine different HLA-G alleles were identified. The HLA-G genotype concordance of G^∗01:01:01/01:04:01 increased the risk of high risk (HR)-HPV genotype positivity in cord blood and infant’s oral mucosa. The mother-child concordance of G^∗01:01:02/01:01:02 increased the risk of oral HPV positivity with HR-HPV genotypes both in the mother and offspring; OR 2.45 (95%CI 1.24–4.85). Discordant HLA-G allele for G^∗01:04:01 and for G^∗01:06 was significantly associated with infant’s oral low risk (LR)-HPV at birth, OR 3.07 (95%CI 1.01–9.36) and OR 5.19 (95%CI 1.22–22.03), respectively. HLA-G had no association with HPV genotype-specific concordance between the mother and child at birth nor influence on perinatal HPV status of the child. Taken together, our results show that HLA-G molecules have a role in predicting the newborn’s likelihood for oral HPV infection at birth.