Avian Influenza Viruses (AIVs) pose today a very significant risk to global health given the widespread circulation of H5N1 highly pathogenic avian influenza viruses (HPAIV). After decimating the avian population all over the world, these viruses spill over to many different mammal species, causing also fatal outbreaks. As the virus continues to evolve increasing human cases of H5N1 HPAIV have been reported, causing concern that these viruses may adapt to the human host and became a pandemic new virus. In order to gain insight into this matter, a detailed phylogenetic analysis of H5N1 HPAIV isolated from humans was performed. A significant number of substitutions have been found in the hemagglutinins (HA) and neuraminidases (NA) among the three H5N1 clades already detected in human cases. Some of these substitutions were found to produce changes in the 3D structure of these proteins. Substitutions providing an evolutionary advantage to replicate or evade the immune response in mammals have been found in several non-structural proteins of strains infecting humans, including regulatory proteins, like PA-X or PB1-F2. A significant degree of polymorphic sites was observed in the proteins of the polymerase complex. The results of these studies are discussed in terms of the evolution of H5N1 HPAIV infecting humans and future work to be done to address the pandemic potential of these viruses.