For his scientific achievements Choi received the New Technology Development Award from the Ministry of Science & Technology (1992), the Special Award from Korean Society for Molecular & Cell Biology from the Korean Society of Molecular and Cellular Biology (1999), the 11th Sangrok Agriculture & Life Science Award from Seoul National University College of Agriculture (2002), the Excellent Monograph Award from the Korean Federation for Science & Technology Societies (2003), the 11th Hwanong Award from Hwanong Academy & Research Foundation (2004), the KSABC Award from the Korean Society for Applied Biology and Chemistry (2006), the 52nd NAS Award from the National Academy of Sciences, and the Top Scientist and Technologist Award of Korea from the Korean Federation of Science and Technology Societies () (2008).