Studied were the pathohistological changes and the morphologic-structural injuries of intestinal mucosa of pigs (5-7 days old), spontaneously affected with rotavirus diarrhea, raised by traditional methods. Simultaneously with the rotavirus invasion was established Isospora suis. In spite of the early time of the disorder (the test was carried out 24 hours after the appearance of the first clinical symptoms) there were established different in degree and expression morphologic changes; atrophy and fusion of the fibrils, replacement of the cylindrical epithelium with cubic, dystrophy and exfoliation of the enterocytes with exposure of the lamina propria. The burden of the dystrophic processes, which has affected the intestinal mycosis, was registered by scanning electronic microscopy. The dystrophic processes start at the top of the intestinal fibrils, the fusion of the fibrils spreads over a big number of them, forming a conglomerate mass. Simultaneously with the fibrils, affected by dystrophy, were observed fibrils with normal shape and size. During immunofluorescent examinations also is observed focal distribution of enterocytes, containing antigen on some of the fibrils. Now is discussed the importance of the pathogenic microflora, in the intestinal track of pigs, raised by traditional methods, for the early appearance and for the burden of the morphologic-structural changes.