Hepatitis E virus (HEV) has become a growing public health concern in industrialized countries. Most of the HEV seroprevalence studies have focused on adult populations, and reports regarding HEV seroepidemiology among children are scarce in these countries. The aims of this work were to perform a nationwide seroprevalence study on HEV infection in Portuguese children and to compare the HEV seropositivity in this 2015 children cohort with results in sera performed 20 years earlier. Sera (N = 352) from children collected in 2015 from all regions of Portugal were screened for anti-HEV IgG and IgM using the commercial enzyme-linked immunosorbent assay recomWell HEV IgG/IgM (2015 version; Mikrogen, Neuried, Germany), and positive samples were retested by immunodot assay recomLine HEV IgG/IgM (2015 version; Mikrogen, Neuried, Germany). For the comparative assessment of HEV seropositivity of the 2 children cohorts, children's sera (N = 71) archived since 1995 were screened for anti-HEV IgG and results were compared with that of the 2015 cohort, matched by sex, age and region. Anti-HEV antibodies were detected in 4 children giving an overall HEV seroprevalence in the 2015 cohort of 1.1%. A healthy 10-15-year-old female was found positive for anti-HEV IgM indicating a current or recent HEV infection. No statistically significant difference was observed in HEV seroprevalence regarding gender, age group and region of residence. Comparison of the HEV seropositivity of the 2 children cohorts showed a statistical significant decrease with time (P = 0.024). This is the first national study of HEV seroprevalence in Portuguese children and the first to demonstrate a decrease of anti-HEV antibodies in this age group over time.