Infection with hepatitis E virus (HEV) leads to acute hepatitis infection in immunocompetent hosts. HEV genotype 3 can present with high frequency and lead to chronic infection in individuals with a compromised immune system. The risk factors related to increased seroprevalence or chronicity in this population are not entirely understood. Moreover, most studies addressing risk factors for HEV in non-endemic areas come from developed areas such as North America and Europe. In this study we evaluated seroprevalence, chronicity and risk factors for HEV in 120 transplant recipients and 88 patients on dialysis in Argentina. We found a significantly higher seroprevalence of HEV IgG in those undergoing dialysis compared with healthy controls (10.2% and 4.3% respectively, p = 0.03). No difference in HEV seroprevalence was observed between healthy controls and transplant recipients (5.8%). We found no association between previously identified risk factors for HEV, such as pork consumption or use of tacrolimus, and HEV seroprevalence. In univariate and multivariate analyses, consumption of fish was associated with higher seroprevalence of HEV (OR = 9.33; 95% CI: 2.07–42.2; p = 0.04). None of the samples showed HEV RNA amplification, indicating that chronicity does not seem to be an issue in these cohorts. Our results show increased seroprevalence of HEV in individuals undergoing dialysis but not in transplant recipients. We also found that fish consumption can be a potential risk factor for acquiring HEV.