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Background: Heteropneustes fossilis (Bloch, 1794) is one of the popular freshwater fish known for its food quality and nutritional value. This study was undertaken with an aim to find out histopathological changes in the intestine of freshwater fish Heteropneustes fossilis, host of trematode parasite Masenia vittatusia Agarwal, 1963. Methods: The intestine of uninfected fish used to determine normal anatomy, while infected intestine to determine pathological changes. The normal histological procedure was followed, which included fixing, rinsing, dehydrating and embedding of tissue. Tissue was cut in 4-6 µm thick sections using a rotary microtome. Haematoxylin and eosin stains were used. Result: The highest damage was observed in the mucosal layer with ruptured and fused microvilli, hyperplasia of villi, damaged columnar epithelium layer and spread of loose connective tissue into the lumen. Other degenerative modifications included hypertrophy of blood vessels in mucosa and muscularis part, some of them ruptured might be the cause of haemorrhage inside the layers. Other changes include variation in the routine shape of all three layers. The mucosal layer showed aggregation of lymphocytes and mast cells as well.