Background: Although many studies have measured HBV cccDNA molecules in Peripheral Blood Mononuclear Cells (PBMC) from patients with active chronic hepatitis B, the current pilot study found PBMC HBV cccDNA in PBMC among HBsAg-positive mothers and their neonates. However, the risk factor of HBV cccDNA in PBMC among HBsAg-positive pregnant female's neonates remains unclear. Objectives: The aim of this study was to explore influential factors of HBV cccDNA in PBMC among HBsAg-positive pregnant female's neonates. Methods: Peripheral blood samples and clinical data were collected from 151 pregnant females, who were positive for hepatitis B surface antigen (HBsAg) in the Third People Hospital of Taiyuan City. Blood samples from 152 neonates were collected before immune prophylaxes administration and tested for HBV markers, HBV DNA in serum, and HBV DNA in PBMC. Bayesian logistic regression with Cauchy prior were used to measure the association between maternal characteristics, neonatal characteristics, and HBV cccDNA in PBMC of neonates. Results: Among neonates of HBsAg-positive mothers, the positive rate of cccDNA in PBMC was 4.61% (7/152). Maternal PBMC HBV cccDNA positivity (OR = 18.411,) and neonates PBMC rcDNA positivity (OR = 13.529, 95% CI: 1.948 -93.690) were associated with HBV cccDNA in neonatal PBMC, respectively. Conclusions: The study suggested that HBV cccDNA can be detected in PBMC of HBsAg-positive mother's neonates. Maternal PBMC HBV cccDNA positivity and neonatal PBMC rcDNA positivity are risk factors of HBV cccDNA in PBMC of neonates.