Flamingo mortalities recorded in Egypt were investigated using parasitological, light, and transmission electron microscopy. During the period 2009-2014, a total of 27 flamingos were examined.Traumatic Myopathy recorded in the major cases 20 cases of 27which appeared as pectrol, superficial and deep leg muscles heamatoma, pulmonary congestion and oedema, swollen kidneys, with a dark cortex. In addition to hepatocellular necrosis and dilatation of liver sinusoids, loss of the glomerular tuft cellularity and necrosis of the proximal convoluted tubules. Sarcosyts (n=2) were observe in the esophagus and intestinal wall of two birds. Blood films stained with Giemsa stain showed the presence of trypanosome sp (one case) between the blood cells. Ehrichliaorganism (n=20) in the cytoplasm of monocytes. Ehrichlia organisms were identified as vacuole micro-colonies (morula) in the spleen and the intestinal muscularis mucosal layer by Transmission electron microscopy. Flamnigolepis liguloides, cestodes (Hymenlopididae) was detected and identified. These cestodes resulted in massive necrosis of intestinal mucosa. Intestinal coccidiosis(n=7) showed severe tissue damage, necrosis and disintegration of glandular epithelial cells, hemorrhage in the sub-mucosa and plenty of schizonts and oocysts. Tetrameriasis were observed in the proventriculs of all birds (n=27) and resulted in atrophy of the proventriculus. Flamingo wing louse was identified as Anaticola phoenicopteri and recorded in all cases (n=27). Amyloidosis recorded in all cases which appeared as Focal amyloidosis of the spleen and associated with spontaneous splenic rupture and suggested altered immune function occurred. It was concluded that the mortality of the migratory flamingo related to multifactorial agents started from the presence of stress, blood parasites, intestinal parasites resulted in several alterations in tissues to be the main causes of mortalities. Moreover, it is recommended to improve their European habitat before migration in order to minimize mortalities.