Highly pathogenic avian influenza virus (HPAIV) subtype H5N1 is circulating in Egypt since 2006, with escalating apprehension about its possibility to become more transmissible amongst humans. In this study, three serial outbreaks of HPAIV H5N1 in domestic Muscovy ducks in Sharkia Governorate, Egypt were investigated. Nervous signs with 62% mortality were observed in Muscovy ducklings. Gross examination revealed severely congested meningeal vessels, hemorrhages on the duodenum, pancreas, and coronary fat. Perivascular lymphocytic cuffing, gliosis and vacuolation of the neuropil were observed in the brain microscopically. Viral antigens were identified in the neurons and the glial cells of the cerebral cortex, submucosal Meissner's plexus neurons of the intestine and the hepatic Kupffer cells by immunohistochemistry. The HPAIV subtype H5N1 was isolated from different duck tissues in 66.7% of examined duck samples. Using RAPD-PCR fingerprinting, there were different patterns in the DNA of Muscovy ducks naturally infected with AIV (24, 48 and 72 hours post appearance of clinical signs) compared to uninfected birds. Differences in RAPD-PCR profiles between infected and uninfected ducks, and genomic instability percent (37.7%±1.76) pointed to the incidence of DNA alterations induced at 24 hours following the appearance of clinical signs. Further in vivo and in vitro experiments need to be done to determine the relative importance of these findings