Managing intellectual property in the context of international development presents many complex decisions regarding research. This paper discusses three key intellectual property management challenges arising from collaborative research projects implemented through the Agricultural Biotechnology for Sustainable Productivity projects, supported by the United States Agency for International Development. The project managers and collaborating scientists are faced with specific challenges regarding intellectual property. For each of these challenges, details are provided on how the collaborating institutions developed an approach to managing intellectual property within the legal framework of the USA and in conjunction with a range of scientific partnerships.