Hepatitis E virus (HEV) infects pigs but does not cause clinical disease in pigs. There is concern that hepatitis E virus from pigs may infect people and that pigs may be an important reservoir for HEV. This study was conducted to get a better understanding of where HEV persists on a pig farm and if there is evidence of contamination of drinking water and nearby surface water with HEV from the pigs. We confirmed the presence of HEV in fresh feces (a pool of feces from 5 pigs per site) collected from the floors of pig barns in 7 of 28 farms and this is consistent with other reports that HEV is common in the swine population. As expected we found more positive farms by sampling concrete pits than by testing fresh feces from the floors in the barns. Demonstration of HEV in pit manure samples of 15 of 28 sites suggests that the virus does survive in pit manure. Only eight of the sites we visited had outdoor lagoons and 3 of these 8 lagoon samples were positive for HEV. Despite exhaustive testing, we were not able to detect the presence of HEV in the drinking water on the sites or in the nearest upstream or downstream surface water sources. This work suggests that HEV is commonly present in fresh pig feces and in manure stored in pits and lagoons on swine farms. HEV detected by RT-PCR in pig manure from storage pits is infectious. However, evidence that HEV from fresh pig feces, pit manure, or lagoon manure is contaminating drinking water supplies or surface water is lacking.