A qualitative risk assessment study was done from January to April 2013. The risk question addressed was “What is the risk of introduction of highly pathogenic avian influenza (HPAI) H5N1 virus to Uganda through wild migratory birds and cross border trade in live poultry and poultry products. The OIE framework for risk assessment was used. Emphasis was, however, laid on exposure assessment. The study involved content analysis of unclassified government reports, key informant interviews and expert opinion consultations. We estimated the risk of introduction of HPAI H5N1 virus through cross border movement of live poultry or poultry products from South Sudan to Uganda as very low with a low level of uncertainty. Furthermore, we also estimated the risk of introduction of HPAI H5N1 to Uganda through migratory wild birds as medium with a high level of uncertainty. The major risk increasing factors for the spread of HPAI H5N1 virus from migratory wild birds to resident poultry and humans included mixing of migratory wild birds with domestic poultry; abundance and spatial distribution of breeding sites; and in some communities, migratory wild birds are hunted and consumed. To prevent introduction of HPAI virus to Uganda, we recommend enhanced veterinary capacity in the whole country; heightened risk-based surveillance programs, especially in the high risk districts; and strengthened biosecurity measures in poultry farms in the high risk districts.