Government, industry and academe have all expressed increased interest in the use of open source software in recent years. We will review some of the open source software tools approved for use at the FDA, with a particular emphasis on the statistical programming language R. From our perspective, R and other open source tools, offer flexible and affordable options which can be employed for research and regulatory activities. R is particularly well suited for graphical applications and for scientific and high performance computing. We believe that open source and proprietary software can be complementary, and that both are useful in achieving the mission of the FDA.