An experiment was carried out for a period of ten months from April 2000 to January 2001 in order to investigate diseases of small indigenous fishes through clinical and histopathological techniques. Fishes like Channa punctatus, Puntius ticto and Nandus nandus were collected from KaiIla beel of Mymensingh area on monthly basis. Clinically and pathologically C. punctatus were more affected than other fish and less affected one was N. nandus. Clinically rough skin, mild necrosis, dermal lesion and discoloration of gill were found in C. punctatus. Rough skin, ill health, red spot in ventral region, skin lesion and necrosis in gill were observed in P. ticto. Weak body, ulcer in ventral region and thick gill filament were seen in N. nandus. The observed pathology were necrosis, pyknosis, inflammation, hemorrhage, hypertrophy, hyperplasia and missing of primary and secondary gill lamelle. Monogenetic trematodes and protozoan cysts were found in gill filaments of all the fish species. Fungal granuloma were observed in skin, muscle and liver of C. punctatus and only skin and muscle of P. ticto and N. nandus. The observed diseases were trichodiniasis, myxoboliasis, dactylogyrosis, gyrodactylosis and epizootic ulcerative syndrome (EUS) in the sampled fish species. It was also found that the external organs like skin and gill were more affected than internal organs such as muscle, liver and kidney. The examined fishes of KaiIla beel were more affected towards the coldest months of the year i.e., December and January, in comparison with other months.