Pharma R&D and the practical application of its results is challenging researchers, developers, professionals and policy makers in Latin America (LA) within the dramatic changes imposed by the world economic crisis. Five generations of R&D are widely recognized up to present time of Knowledge Management but LA countries are between the 2nd and 3rd generations. Non-wealthy countries cannot afford the Fifth Generation because the lack of managerial experience and both financial and human resources, and the phenomenon that most of the present knowledge in advanced technologies are private-owned due to intellectual property rights, mainly in highly developed countries as USA, Japan and West Europe countries. However, a possibility exists for those LA countries in terms of the Second and Third Generations of R&D, where several key factors must be considered within the pharma sector. This work focuses on factors influencing Pharma R&D in LA like funding (in terms of GDP percentage), protective environment of national pharma sector, human resources, technological dependence from abroad, and managerial capacity in terms of the existence of R&D Strategic Planning and Project Portfolio as a way to set an innovative policy. Challenges and opportunities for the Pharma R&D in LA are discussed within the frame of the health sector.