ObjectivesA systematic review of multidisciplinary studies on Japanese encephalitis (JE) in the Philippines indicated that endemic foci may be found in all 17 administrative regions in the country. MethodsTo establish the etiology of the disease, virus detection and seroprevalence surveys in 198 pigs were conducted in 2010–2011 in four barangays (villages) in the Municipality of San Jose, Tarlac. Prior to the present study, JE virus genotype III (JEV GIII) was recovered from the mosquito, Culex tritaeniorhynchus, in the same municipality where backyard hog-raising and wet rice cultivation were common practices among households located within 1 km radius from the paddies. ResultsJEV GIII was detected from serum and nasal swabs from pigs, 3 to 5-month-old, from barangays Pao, Moriones, and Villa Aglipay. Immunoglobulin (Ig) M and IgG were measured by enzyme-linked immunosorbent assay in pigs < 4 to > 8 months old, with an overall total of 17.2 % and 62.1 %, respectively. The presence of these antibodies in all pigs during four observation periods indicated year-round transmission starting with the rainy season, which encompasses the months of July and September 2010. IgM represented new infections. IgG increased correspondingly with age with repeated infections in older pigs. IgG levels remained high in all barangays. The number of households with any one of the markers: IgM, IgG, reverse transcription-polymerase chain reaction averaged out at 82.5 %, reflecting as it were, vulnerability to JE in barangays where all 198 pigs were examined. This report contributes to knowledge on JE, whereby incidence in humans may be linked to its epizootic spillover from pigs. ConclusionsThe study has shown that four barangays, representing a rice-farming community, supported the enzootic cycle of JE in swine, with mosquitoes previously found to be infected with JEV GIII in San Jose. Thus, infected pigs, rainfall, and proximity of human habitation to breeding sites of vector mosquitoes constituted the risk factors for JE, as it were in other endemic countries in Asia. The finding of viral RNA in nasal swabs suggests the possibility of direct transmission among pigs via the oronasal route. From the standpoint of public health, JE immunization of children and periodic surveillance of swine are recommended.