Autochthonous hepatitis E virus (HEV) strains have been described infecting populations of industrialized countries, previously considered as non-endemic areas. The HEV strains circulating in one of those areas in south-western Europe (Barcelona, Spain) have been studied by analysing amplicons obtained from HEV genomes identified in wastewater, biosolids and sludge. Six sewage and two biosolid HEV positive samples from urban wastewater treatment plants and two positive HEV sludge samples with animal contamination were analysed by cloning and sequencing of 10–12 clones per sample. The results proved the presence of HEV strains belonging to genotype 3 and also sporadically to genotype 1 in urban sewage and biosolids, showing the simultaneous circulation of diverse HEV strains in the human population of the studied area. Only HEV genotype 3 was identified in slaughterhouse sludge samples. The circulation of genotype 1 in industrialized areas may have further health implications since this genotype has been associated with important epidemics in developing areas. Contamination of food and water through their contact with sewage not properly treated and biosolids presenting HEV may represent a significant risk for human populations in relation to HEV even in industrialized areas.