In the present study, the histological structures of the liver, intestine, stomach and ovary of Lates niloticus from Lake Nasser (Kalabsha station) were studied during spring season, 2013. Several histopathological changes were observed in liver, intestine, stomach and ovary of the studied fish. In the liver, vacuolar degeneration, focal areas of necrosis, destruction of hepatoportal blood vessels and haemorrhage between the hepatocytes were observed. Besides, intravascular haemolysis and dilation and congestion were noticed in sinusoids. The histological changes in stomach and intestine included fused villi, the outer membrane of villi were broken, hemorrhage in the sub mucosa region and cells swelling. In the ovary, degenerative and atretic oocytes, proliferative changes in the granulosa of the oocytes, haemorrhage between the oocytes and intravascular haemolysis in some ovarian blood vessels were seen.