Three of 10 piglets with watery diarrhea, aged 24, 21 and 22 days (cases 1, 2 and 3, respectively), were investigated in detail after euthanasia (as the remaining seven recovered without specific treatment). Enterococcal bacteria were isolated and multilocus sequence analysis showed 100% and 99% identity with the phenylalanyl tRNA synthase and RNA polymerase α subunit genes of strains of Enterococcus villorum, respectively. Histologically, severe epithelial desquamation, atrophy, and regeneration of ileal villi were observed in cases 1, 2 and 3, respectively. The number of bacteria was large in case 1, smaller in case 2, and sparse in case 3. These findings suggest that case 1 was at an earlier stage of enteropathy than case 2, and that case 3 was recovering. In case 1, the exfoliation of epithelial cells with many bacteria into the intestinal lumen was interpreted as a host reaction for eradicating marginally pathogenic enteroadherent bacteria. Folded smooth muscle cells and intact blood and lymphatic vessels in the atrophic lamina propria may have been linked to the rapid regeneration of villi.