This article addresses the following issues: How did external funding of Flemish academic research develop during the 1980's and early 1990's? What are the effects of the increase of external funding on the size and the composition of the research capacity in Flemish universities, and on research performance as reflected in bibliometric indicators? We present results of a quantitative analysis of 340 research departments in the natural and life sciences at three Flemish universities. We found that the externally funded research capacity increased strongly and is more and more concentrated in a limited number of departments. Departments with a high international standing have profited more from external funds than groups with a low impact. In the class of departments showing the strongest increase in the externally funded research capacity, the ratio of the number of junior and senior scientists in these departments increased radically, while the publication productivity decreased. Our findings point towards the problem that if these trends continue to develop, a situation may emerge in which the basis normally provided by the university itself has become too small for externally funded research activities.