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Hepatitis E virus ( HEV ) genotype 3 ( HEV 3) is distributed globally and infects both humans and animals, mainly domestic pigs and wild boars, which are the major reservoirs. In this study, the prevalence of  HEV  among Swedish pigs was investigated by  HEV RNA  analysis in 363 faecal samples from 3‐month‐old piglets sampled twice (2013 and 2014) in 30 Swedish pig farms. Four different types of farms were investigated; organic, conventional closed (keeping the sow), satellites in a sow pool (conventional farms sharing sows) and conventional non‐closed farms (purchasing gilts). More than two‐thirds (77%) of the farms had  HEV ‐infected pigs.  HEV RNA  was found in faeces from 79 pigs (22%). Partial  ORF 1 could be sequenced in 46 strains. Phylogenetic analysis revealed a unique  HEV 3 strain for each farm. Strains sampled more than a year apart from the same farm were closely related, indicating that the same  HEV  strain is present for several years on the farm. Despite that only 4% of the Swedish pig farms were investigated, two farms had strains similar to those from humans, another had strains similar to wild boar  HEV . The uniqueness of strains from each farm indicates a possibility to identify a source of infection down to farm level. This knowledge may be used by the farms to investigate the effectiveness of good hygiene routines to reduce the amount of  HEV  and thus the infection risk in the farm, and for Swedish public health authorities to identify cases of  HEV  transmissions from consumption of uncooked pork.

Hepatitis E virus strains infecting Swedish domestic pigs are unique for each pig farm and remain in the farm for at least 2 years