In 1996, the CSJ and ACS established a cooperative exchange in the areas of organic chemistry, bioorganic chemistry, and related topics in commemoration of Koji Nakanishi of Columbia University, New York. A bilateral symposium is held every year on a reciprocal basis, and a Nakanishi Prize is awarded during each symposium. Since 2000, the symposium has been held at the CSJ Spring Meeting. Occasionally more than 400 people attend.

To date, the following are recipients of the Nakanishi Prize:

1996 Yoshimasa Hirata (Professor Emeritus of Nagoya University)
1997 Frank H. Westheimer (Professor Emeritus of Harvard University)
1998 Albert Eschenmoser (Professor Emeritus of ETH)
1999 Jeremy Knowles (Harvard University)
2000 Satoshi Omura (Kitasato Research Laboratory)
2001 John D. Roberts (Professor Emeritus of Caltech)
2002 Sir Jack E. Baldwin (Oxford University)