OBJECTIVE This study aimed to survey the prevalence and incidence of hepatitis B (HBV) and hepatitis C virus (HCV) infection among elementary school students in Siem Reap province, Cambodia and to evaluate the effects of a national infant HBV vaccination program introduced in 2001. METHODS Students in 3rd grade during the 2011, 2012, and 2013 academic years were enrolled in this study; at the time of the second examination, in the 2014-2015 academic year, the students were in 5th or 6th grade. The incidence and prevalence rates of HBV and HCV infection were estimated and full HBV sequences were analyzed. RESULTS Among 248 students (107 male and 141 female) born between 1999 and 2005, five students were HBV surface antigen (HBs-Ag) positive (2.02%), and all of them were infected with genotype C. Among them, subgenotype C1 was found in four students and, unexpectedly, complete genetic sequence identity of subgenotype C1 was found in two students from different families. The anti-HBV core (HBc) and anti-HBs prevalence rates were 10.89% and 16.13%, respectively. Twenty-five students were positive for anti-HBs and negative for both HBsAg and anti-HBc (10.08%; estimated serological vaccination rate); this rate increased significantly with the birth year (P = 0.0229). Prevalence of anti-HCV was 2.82%, and HCV RNA was not detected. The estimated incidence of HBV and HCV infection were both 0/1000 person-years (PY) (95% confidence interval, 0-20.61/1000 PY and 0-14.50/1000 PY, respectively). CONCLUSIONS Hepatitis B virus full-genome sequencing and serological analysis revealed the possibility of horizontal transmission of HBV among Cambodian schoolchildren. However, the anti-HBc positivity rate decreased along with increasing age and estimated serological vaccination rates.