Following the incorporation of Japanese national universities in April 2004, the ownership of university inventions is now similar to that in the USA. However, in contrast to the USA, joint research projects involving close collaboration with company researchers who are frequently named as co-inventors are common. A large proportion of university discoveries are passed directly to established companies under joint research agreements. This perpetuates the pre-2004 situation. It also raises concerns that large companies are pre-empting publicly funded discoveries and decreasing opportunities for new company formation. An analysis of inventions reported to a major national university indicates that one-third are attributed to joint research, and, among those inventions for which patent applications are filed, the proportion is still higher. The corresponding proportions at most other major universities are probably even higher than at this university. Pre-emption by large companies is more common in engineering and materials/chemistry than in the life sciences. Further cross-national comparisons are needed to assess the impact on innovation and basic research of the Japanese and US models of university-industry cooperation, and to guide policy. (Contains 6 figures and 31 notes.)