Postweaning diarrhea and wasting are a major concern in pig farms’ management. Although hemolytic enterotoxigenic Escherichia coli, porcine epidemic diarrhea virus, porcine circovirus type 2, and Salmonella spp. are the most frequent etiological agents of these diseases, Entamoeba suis and E. polecki were recently reported to be associated with diarrhea in pigs. Since the infection rate of Entamoeba in pigs and its relationship with other pathogens are unknown, we examined 206 pigs exhibiting diarrhea and/or wasting in Aichi Prefecture, Japan to determine the prevalence of porcine Entamoeba spp. E. suis- and E. polecki-like trophozoites were detected by histopathology in 53 pigs, mainly in the lumen of the large intestine. Ulcerative colitis with infiltrating trophozoites was observed in 16 pigs, and most of these trophozoites were identified as E. polecki subtype 3 by PCR and sequence analysis. Tissue-invasive Entamoeba spp. were prevalent in pigs exhibiting diarrhea and wasting, and most samples were also positive for either Salmonella spp. or Lawsonia intracellularis by immunohistochemistry. These Results suggested that Entamoeba was widespread in farms in Aichi Prefecture, and in most cases, enteritis was caused by co-infection by Entamoeba with Salmonella spp. or L. intracellularis, which causes wasting by exacerbating the original mucosal lesions.