Background: Hepatitis E virus (HEV) infection is a significant public health concern in Asia, and swine is an important source of sporadic HEV infection in human. However, no epidemiological data are available regarding HEV infection among the swine or human population in the Philippines. To assess the HEV infection status among pigs in rural areas, we investigated the molecular characteristics and seroprevalence of HEV among household-raised pigs in San Jose, Tarlac Province, the Philippines. Result: Serum and rectal swab samples were collected from 299 pigs aged 2-24 months from 155 households in four barangays (villages) between July 2010 and June 2011. Enzyme-linked immunosorbent assay (ELISA) revealed that 50.3% [95% confidence interval (CI) 44.5-56.2%] and 22.9% (95% CI 18.2-28.1%) of pigs tested positive for anti-HEV IgG and IgM, respectively. HEV RNA was detected in the feces of 22 pigs (7.4%, 95% CI 4.7-10.9%). A total of 103 households (66.5%, 95% CI 58.4-73.8%) had at least one pig that tested positive for anti-HEV IgG or IgM or HEV RNA. The prevalence of anti-HEV IgG and IgM in breeding pig (8-24 months) were higher than that in growing pigs (2-4 months) (p<0.0001 and p=0.008, respectively). HEV RNA was more frequently detected in 2-4-month-old pigs (9.2%, 95% CI 5.4-14.6%) than in ≥5-month-old pigs (4.8%, 95% CI 1.1-8.5%) without statistical significance (p=0.142). HEV RNA showed 0-27.6% nucleotide difference at the partial ORF2 gene among the detected viruses, and a majority of them belonged to subtype 3a (20/22, 90.9%). Conclusion: We found a high prevalence of HEV antibodies in the household-raised pig population in rural areas of the Philippines, which indicates the potential risk of HEV infection among local residents. Only genotype 3 of HEV was observed, and genetically diverse strains of HEV were found to be circulating in pigs in this study.