Recently, a novel deoxyribonucleic acid (DNA) virus, designated SEN virus (SENV), was discovered and strong associations between the two SENV variants (SENV-D and SENV-H) and non-A to E hepatitis were reported. To clarify the character of SENV infection in children, we investigated the detection rates of serum SENV DNA by polymerase chain reaction (PCR) among children with non-A to C hepatitis, with histories of transfusions, with neither histories of transfusions nor liver diseases (control), and among pregnant women. SENV-D was detected in 60% of fulminant hepatitis, 5% of acute hepatitis, 11% of chronic hepatitis, 13% of controls, and 15% of pregnant women. SENV-H was detected in none of fulminant hepatitis, 5% of acute hepatitis, none of chronic hepatitis, 2% of controls, and 12% of pregnant women. No significant difference was found for SENV-D between acute or chronic hepatitis and controls, however SENV-D detection rate in fulminant hepatitis was significantly higher than that in controls (P < 0.05). No significant difference was found for SENV-H between any hepatitis and controls, however SENV-H detection rate in pregnant women was significantly higher than that in controls (P < 0.05). Neither SENV-D nor SENV-H was associated with acute or chronic hepatitis; however, SENV-D might be a risk factor of fulminant hepatitis.