Policy problems of prototype costing at research universities are discussed, based on a case study of a clinical treatment prototype program at a research university hospital. Prototypes programs generate reproducible knowledge with useful applications and are primarily developed in professional schools. The potential of using costing prototypes and characteristics of research universities that affect costing systems are considered. The case study involved a cost effectiveness study that used longitudinal microdata to track the effects of treatment. Experimental clinical treatment was provided for children at a major research university medical center. The children were observed for clinical symptoms (e.g., aggression, depression) at the time of admission, discharge, and followup. The clinical program was effective despite, not because of the university's internal management. Weak institutional integration caused by the highly decentralized university structure compounded the problems generated by concern for external compliance. Isolated departmental subcultures created conflict instead of cooperation, leading to higher transactions costs and diminishing productivity. (SW)